From ff23473e827a4efa59826d6c954145005e69cb10 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 16:02:58 +0000 Subject: [PATCH 01/15] Restructure tests to run individually for each module --- tests/software/bowtie/align/main.nf | 29 +++++ tests/software/bowtie/align/test.yml | 47 ++++++++ tests/software/bowtie/build/main.nf | 10 ++ tests/software/bowtie/build/test.yml | 18 +++ tests/software/bowtie2/align/main.nf | 29 +++++ tests/software/bowtie2/align/test.yml | 45 ++++++++ tests/software/bowtie2/build/main.nf | 10 ++ tests/software/bowtie2/build/test.yml | 18 +++ tests/software/bwa/index/main.nf | 9 ++ tests/software/bwa/index/test.yml | 14 +++ tests/software/bwa/mem/main.nf | 38 +++++++ tests/software/bwa/mem/test.yml | 19 ++++ tests/software/cutadapt/main.nf | 8 +- tests/software/cutadapt/test.yml | 12 +- tests/software/dsh/filterbed/main.nf | 14 +++ tests/software/dsh/filterbed/test.yml | 8 ++ tests/software/dsh/splitbed/main.nf | 14 +++ tests/software/dsh/splitbed/test.yml | 10 ++ tests/software/fastp/main.nf | 11 +- tests/software/fastp/test.yml | 12 +- tests/software/fastqc/main.nf | 18 +-- tests/software/fastqc/test.yml | 10 +- tests/software/gffread/test.yml | 2 +- tests/software/multiqc/test.yml | 2 +- .../picard/collectmultiplemetrics/main.nf | 17 +++ .../picard/collectmultiplemetrics/test.yml | 16 +++ tests/software/picard/markduplicates/main.nf | 23 ++++ tests/software/picard/markduplicates/test.yml | 17 +++ tests/software/picard/mergesamfiles/main.nf | 15 +++ tests/software/picard/mergesamfiles/test.yml | 8 ++ tests/software/preseq/lcextrap/main.nf | 29 +++++ tests/software/preseq/lcextrap/test.yml | 21 ++++ tests/software/quast/test.yml | 4 +- tests/software/salmon/index/main.nf | 11 ++ tests/software/salmon/index/test.yml | 31 +++++ tests/software/salmon/quant/main.nf | 33 ++++++ tests/software/salmon/quant/test.yml | 107 ++++++++++++++++++ tests/software/samtools/flagstat/main.nf | 14 +++ tests/software/samtools/flagstat/test.yml | 8 ++ tests/software/samtools/idxstats/main.nf | 14 +++ tests/software/samtools/idxstats/test.yml | 8 ++ tests/software/samtools/index/main.nf | 13 +++ tests/software/samtools/index/test.yml | 8 ++ tests/software/samtools/mpileup/main.nf | 15 +++ tests/software/samtools/mpileup/test.yml | 8 ++ tests/software/samtools/sort/main.nf | 13 +++ tests/software/samtools/sort/test.yml | 8 ++ tests/software/samtools/stats/main.nf | 14 +++ tests/software/samtools/stats/test.yml | 8 ++ tests/software/samtools/view/main.nf | 13 +++ tests/software/samtools/view/test.yml | 8 ++ tests/software/seacr/callpeak/main.nf | 15 +++ tests/software/seacr/callpeak/test.yml | 8 ++ tests/software/star/align/main.nf | 29 +++++ tests/software/star/align/test.yml | 75 ++++++++++++ tests/software/star/genomegenerate/main.nf | 12 ++ tests/software/star/genomegenerate/test.yml | 32 ++++++ tests/software/stringtie/test.yml | 4 +- tests/software/trimgalore/main.nf | 17 +-- tests/software/trimgalore/test.yml | 4 +- tests/software/ucsc/bedgraphtobigwig/main.nf | 16 +++ tests/software/ucsc/bedgraphtobigwig/test.yml | 7 ++ 62 files changed, 1049 insertions(+), 61 deletions(-) create mode 100644 tests/software/bowtie/align/main.nf create mode 100644 tests/software/bowtie/align/test.yml create mode 100644 tests/software/bowtie/build/main.nf create mode 100644 tests/software/bowtie/build/test.yml create mode 100644 tests/software/bowtie2/align/main.nf create mode 100644 tests/software/bowtie2/align/test.yml create mode 100644 tests/software/bowtie2/build/main.nf create mode 100644 tests/software/bowtie2/build/test.yml create mode 100644 tests/software/bwa/index/main.nf create mode 100644 tests/software/bwa/index/test.yml create mode 100644 tests/software/bwa/mem/main.nf create mode 100644 tests/software/bwa/mem/test.yml create mode 100644 tests/software/dsh/filterbed/main.nf create mode 100644 tests/software/dsh/filterbed/test.yml create mode 100644 tests/software/dsh/splitbed/main.nf create mode 100644 tests/software/dsh/splitbed/test.yml create mode 100644 tests/software/picard/collectmultiplemetrics/main.nf create mode 100644 tests/software/picard/collectmultiplemetrics/test.yml create mode 100644 tests/software/picard/markduplicates/main.nf create mode 100644 tests/software/picard/markduplicates/test.yml create mode 100644 tests/software/picard/mergesamfiles/main.nf create mode 100644 tests/software/picard/mergesamfiles/test.yml create mode 100644 tests/software/preseq/lcextrap/main.nf create mode 100644 tests/software/preseq/lcextrap/test.yml create mode 100644 tests/software/salmon/index/main.nf create mode 100644 tests/software/salmon/index/test.yml create mode 100644 tests/software/salmon/quant/main.nf create mode 100644 tests/software/salmon/quant/test.yml create mode 100644 tests/software/samtools/flagstat/main.nf create mode 100644 tests/software/samtools/flagstat/test.yml create mode 100644 tests/software/samtools/idxstats/main.nf create mode 100644 tests/software/samtools/idxstats/test.yml create mode 100644 tests/software/samtools/index/main.nf create mode 100644 tests/software/samtools/index/test.yml create mode 100644 tests/software/samtools/mpileup/main.nf create mode 100644 tests/software/samtools/mpileup/test.yml create mode 100644 tests/software/samtools/sort/main.nf create mode 100644 tests/software/samtools/sort/test.yml create mode 100644 tests/software/samtools/stats/main.nf create mode 100644 tests/software/samtools/stats/test.yml create mode 100644 tests/software/samtools/view/main.nf create mode 100644 tests/software/samtools/view/test.yml create mode 100644 tests/software/seacr/callpeak/main.nf create mode 100644 tests/software/seacr/callpeak/test.yml create mode 100644 tests/software/star/align/main.nf create mode 100644 tests/software/star/align/test.yml create mode 100644 tests/software/star/genomegenerate/main.nf create mode 100644 tests/software/star/genomegenerate/test.yml create mode 100644 tests/software/ucsc/bedgraphtobigwig/main.nf create mode 100644 tests/software/ucsc/bedgraphtobigwig/test.yml diff --git a/tests/software/bowtie/align/main.nf b/tests/software/bowtie/align/main.nf new file mode 100644 index 00000000..c31d5e2d --- /dev/null +++ b/tests/software/bowtie/align/main.nf @@ -0,0 +1,29 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] ) +include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] ) + +workflow test_bowtie_alignment_single_end { + + def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + BOWTIE_BUILD ( fasta ) + + def input = [] + input = [ [ id:'test', single_end:true ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ] + BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index ) +} + +workflow test_bowtie_alignment_paired_end { + + def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + BOWTIE_BUILD ( fasta ) + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] + BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index ) +} diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml new file mode 100644 index 00000000..0824644e --- /dev/null +++ b/tests/software/bowtie/align/test.yml @@ -0,0 +1,47 @@ +- name: bowtie align single-end + command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config + tags: + - bowtie + - bowtie_align + - bowtie_align_single_end + files: + - path: output/bowtie/bowtie/NC_010473.1.ebwt + md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c + - path: output/bowtie/bowtie/NC_010473.2.ebwt + md5sum: bfd10c5319c6a0dbc540fd789254a5dd + - path: output/bowtie/bowtie/NC_010473.3.ebwt + md5sum: cd201e81724f3099131aec16ef2cc53b + - path: output/bowtie/bowtie/NC_010473.4.ebwt + md5sum: bbb9d6d21ad765d135f95290204e8433 + - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt + md5sum: 44f719c2fe42e1f35d54e798775846d1 + - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt + md5sum: f3c398bba5158f4039334a932d79c051 + - path: output/bowtie/test.out + md5sum: a81cb18024616415a6cec3108a36fccd + - path: output/bowtie/test.bam + md5sum: 9feed8a55d4b5e600dcc577768ef07fc + +- name: bowtie align paired-end + command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config + tags: + - bowtie + - bowtie_align + - bowtie_align_paired_end + files: + - path: output/bowtie/bowtie/NC_010473.1.ebwt + md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c + - path: output/bowtie/bowtie/NC_010473.2.ebwt + md5sum: bfd10c5319c6a0dbc540fd789254a5dd + - path: output/bowtie/bowtie/NC_010473.3.ebwt + md5sum: cd201e81724f3099131aec16ef2cc53b + - path: output/bowtie/bowtie/NC_010473.4.ebwt + md5sum: bbb9d6d21ad765d135f95290204e8433 + - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt + md5sum: 44f719c2fe42e1f35d54e798775846d1 + - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt + md5sum: f3c398bba5158f4039334a932d79c051 + - path: output/bowtie/test.out + md5sum: a23e9a2a76e949aeb3693bcfae41a615 + - path: output/bowtie/test.bam + md5sum: cf6a6381aa504e8342638ff3b509721e diff --git a/tests/software/bowtie/build/main.nf b/tests/software/bowtie/build/main.nf new file mode 100644 index 00000000..4b43eb87 --- /dev/null +++ b/tests/software/bowtie/build/main.nf @@ -0,0 +1,10 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] ) + +workflow test_bowtie_build { + fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + BOWTIE_BUILD ( fasta ) +} \ No newline at end of file diff --git a/tests/software/bowtie/build/test.yml b/tests/software/bowtie/build/test.yml new file mode 100644 index 00000000..145836d6 --- /dev/null +++ b/tests/software/bowtie/build/test.yml @@ -0,0 +1,18 @@ +- name: bowtie build + command: nextflow run ./tests/software/bowtie -entry test_bowtie_build -c tests/config/nextflow.config + tags: + - bowtie + - bowtie_build + files: + - path: output/bowtie/bowtie/NC_010473.1.ebwt + md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c + - path: output/bowtie/bowtie/NC_010473.2.ebwt + md5sum: bfd10c5319c6a0dbc540fd789254a5dd + - path: output/bowtie/bowtie/NC_010473.3.ebwt + md5sum: cd201e81724f3099131aec16ef2cc53b + - path: output/bowtie/bowtie/NC_010473.4.ebwt + md5sum: bbb9d6d21ad765d135f95290204e8433 + - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt + md5sum: 44f719c2fe42e1f35d54e798775846d1 + - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt + md5sum: f3c398bba5158f4039334a932d79c051 \ No newline at end of file diff --git a/tests/software/bowtie2/align/main.nf b/tests/software/bowtie2/align/main.nf new file mode 100644 index 00000000..89e9f250 --- /dev/null +++ b/tests/software/bowtie2/align/main.nf @@ -0,0 +1,29 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] ) +include { BOWTIE2_ALIGN } from '../../../software/bowtie2/align/main.nf' addParams( options: [:] ) + +workflow test_bowtie2_align_single_end { + + def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + BOWTIE2_BUILD ( fasta ) + + def input = [] + input = [ [ id:'test', single_end:true ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ] + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index ) +} + +workflow test_bowtie2_align_paired_end { + + def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + BOWTIE2_BUILD ( fasta ) + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index ) +} diff --git a/tests/software/bowtie2/align/test.yml b/tests/software/bowtie2/align/test.yml new file mode 100644 index 00000000..2e9e3279 --- /dev/null +++ b/tests/software/bowtie2/align/test.yml @@ -0,0 +1,45 @@ +- name: bowtie2 align single-end + command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_align_single_end -c tests/config/nextflow.config + tags: + - bowtie2 + - bowtie2_align_single_end + files: + - path: output/bowtie2/bowtie2/NC_010473.1.bt2 + md5sum: 4db22d92e72111a5fbf609b3d9a43015 + - path: output/bowtie2/bowtie2/NC_010473.2.bt2 + md5sum: f4429ec74ee0064732c4bb26718a3eb1 + - path: output/bowtie2/bowtie2/NC_010473.3.bt2 + md5sum: cd201e81724f3099131aec16ef2cc53b + - path: output/bowtie2/bowtie2/NC_010473.4.bt2 + md5sum: bbb9d6d21ad765d135f95290204e8433 + - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 + md5sum: 4ccfee8857c3b1c69857e5ecdef597aa + - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 + md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 + - path: output/bowtie2/test.bowtie2.log + md5sum: 90041c264231be535042adb93a279356 + - path: output/bowtie2/test.bam + md5sum: 906102f401d8234b6473790988fb09cf + +- name: bowtie2 align paired-end + command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config + tags: + - bowtie2 + - bowtie2_align_paired_end + files: + - path: output/bowtie2/bowtie2/NC_010473.1.bt2 + md5sum: 4db22d92e72111a5fbf609b3d9a43015 + - path: output/bowtie2/bowtie2/NC_010473.2.bt2 + md5sum: f4429ec74ee0064732c4bb26718a3eb1 + - path: output/bowtie2/bowtie2/NC_010473.3.bt2 + md5sum: cd201e81724f3099131aec16ef2cc53b + - path: output/bowtie2/bowtie2/NC_010473.4.bt2 + md5sum: bbb9d6d21ad765d135f95290204e8433 + - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 + md5sum: 4ccfee8857c3b1c69857e5ecdef597aa + - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 + md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 + - path: output/bowtie2/test.bowtie2.log + md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5 + - path: output/bowtie2/test.bam + md5sum: 732a33cd9816b38ea9b919c25eeb78f8 diff --git a/tests/software/bowtie2/build/main.nf b/tests/software/bowtie2/build/main.nf new file mode 100644 index 00000000..9742d3ce --- /dev/null +++ b/tests/software/bowtie2/build/main.nf @@ -0,0 +1,10 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] ) + +workflow test_bowtie2_build { + fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + BOWTIE2_BUILD ( fasta ) +} \ No newline at end of file diff --git a/tests/software/bowtie2/build/test.yml b/tests/software/bowtie2/build/test.yml new file mode 100644 index 00000000..0c01844b --- /dev/null +++ b/tests/software/bowtie2/build/test.yml @@ -0,0 +1,18 @@ +- name: bowtie2 build + command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_build -c tests/config/nextflow.config + tags: + - bowtie2 + - bowtie2_build + files: + - path: output/bowtie2/bowtie2/NC_010473.1.bt2 + md5sum: 4db22d92e72111a5fbf609b3d9a43015 + - path: output/bowtie2/bowtie2/NC_010473.2.bt2 + md5sum: f4429ec74ee0064732c4bb26718a3eb1 + - path: output/bowtie2/bowtie2/NC_010473.3.bt2 + md5sum: cd201e81724f3099131aec16ef2cc53b + - path: output/bowtie2/bowtie2/NC_010473.4.bt2 + md5sum: bbb9d6d21ad765d135f95290204e8433 + - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 + md5sum: 4ccfee8857c3b1c69857e5ecdef597aa + - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 + md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 \ No newline at end of file diff --git a/tests/software/bwa/index/main.nf b/tests/software/bwa/index/main.nf new file mode 100644 index 00000000..93510a21 --- /dev/null +++ b/tests/software/bwa/index/main.nf @@ -0,0 +1,9 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] ) + +workflow test_bwa_index { + BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ) +} \ No newline at end of file diff --git a/tests/software/bwa/index/test.yml b/tests/software/bwa/index/test.yml new file mode 100644 index 00000000..29d50d9b --- /dev/null +++ b/tests/software/bwa/index/test.yml @@ -0,0 +1,14 @@ +- name: bwa index + command: nextflow run ./tests/software/bwa -entry test_bwa_index -c tests/config/nextflow.config + tags: + - bwa + - bwa_index + files: + - path: output/bwa/NC_010473.fa.amb + md5sum: 942a990ae872f1c0b8d72dda2db405d5 + - path: output/bwa/NC_010473.fa.bwt + md5sum: 7301b52e2ecb893d429a49fa692447ae + - path: output/bwa/NC_010473.fa.pac + md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad + - path: output/bwa/NC_010473.fa.sa + md5sum: a47dcc92e750e2f16fbd979b8ff9538e \ No newline at end of file diff --git a/tests/software/bwa/mem/main.nf b/tests/software/bwa/mem/main.nf new file mode 100644 index 00000000..0324546d --- /dev/null +++ b/tests/software/bwa/mem/main.nf @@ -0,0 +1,38 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { BWA_MEM } from '../../../software/bwa/mem/main.nf' addParams( options: [:] ) + +/* + * Test with single-end data + */ +workflow test_bwa_mem_single_end { + + def input = [] + input = [ [ id:'test', single_end:true ], // meta map + [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ] + + BWA_MEM ( + input, + file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true), + file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + ) +} + +/* + * Test with paired-end data + */ +workflow test_bwa_mem_paired_end { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ] + + BWA_MEM ( + input, + file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true), + file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + ) +} diff --git a/tests/software/bwa/mem/test.yml b/tests/software/bwa/mem/test.yml new file mode 100644 index 00000000..8c726066 --- /dev/null +++ b/tests/software/bwa/mem/test.yml @@ -0,0 +1,19 @@ +- name: bwa mem single-end + command: nextflow run ./tests/software/bwa -entry test_bwa_mem_single_end -c tests/config/nextflow.config + tags: + - bwa + - bwa_mem + - bwa_mem_single_end + files: + - path: output/test_single_end/test.bam + md5sum: 3ee21210bac387e0335008146e4728bc + +- name: bwa mem paired-end + command: nextflow run ./tests/software/bwa -entry test_bwa_mem_paired_end -c tests/config/nextflow.config + tags: + - bwa + - bwa_mem + - bwa_mem_paired_end + files: + - path: output/test_paired_end/test.bam + md5sum: 510d8acc6448c07cdacce8e64ec0904c diff --git a/tests/software/cutadapt/main.nf b/tests/software/cutadapt/main.nf index fb3b5c52..bd632694 100644 --- a/tests/software/cutadapt/main.nf +++ b/tests/software/cutadapt/main.nf @@ -7,11 +7,11 @@ include { CUTADAPT } from '../../../software/cutadapt/main.nf' addParams( optio /* * Test with single-end data */ -workflow test_cutadapt_se { +workflow test_cutadapt_single_end { + def input = [] input = [ [ id:'test', single_end:true ], // meta map [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ] - CUTADAPT( input ) } @@ -19,12 +19,12 @@ workflow test_cutadapt_se { * Test with paired-end data */ -workflow test_cutadapt_pe { +workflow test_cutadapt_paired_end { + def input = [] input = [ [ id:'test', single_end:false ], // meta map [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] - CUTADAPT( input ) } diff --git a/tests/software/cutadapt/test.yml b/tests/software/cutadapt/test.yml index c91a0713..9cadf0fb 100644 --- a/tests/software/cutadapt/test.yml +++ b/tests/software/cutadapt/test.yml @@ -1,17 +1,17 @@ -- name: Run cutadapt single-end test workflow - command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_se -c tests/config/nextflow.config +- name: cutadapt single-end + command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_single_end -c tests/config/nextflow.config tags: - cutadapt - - cutadapt_se + - cutadapt_single_end files: - path: ./output/cutadapt/test.cutadapt.log - path: ./output/cutadapt/test.trim.fastq.gz -- name: Run cutadapt paired-end test workflow - command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_pe -c tests/config/nextflow.config +- name: cutadapt paired-end + command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_paired_end -c tests/config/nextflow.config tags: - cutadapt - - cutadapt_pe + - cutadapt_paired_end files: - path: ./output/cutadapt/test.cutadapt.log - path: ./output/cutadapt/test_1.trim.fastq.gz diff --git a/tests/software/dsh/filterbed/main.nf b/tests/software/dsh/filterbed/main.nf new file mode 100644 index 00000000..f4d63496 --- /dev/null +++ b/tests/software/dsh/filterbed/main.nf @@ -0,0 +1,14 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { DSH_FILTERBED } from '../../../software/dsh/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] ) + +workflow test_dsh_filterbed { + + def input = [] + input = [ [ id:'A' ], // meta map + [ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ] + + DSH_FILTERBED ( input ) +} \ No newline at end of file diff --git a/tests/software/dsh/filterbed/test.yml b/tests/software/dsh/filterbed/test.yml new file mode 100644 index 00000000..989da517 --- /dev/null +++ b/tests/software/dsh/filterbed/test.yml @@ -0,0 +1,8 @@ +- name: dsh filterbed + command: nextflow run ./tests/software/dsh -entry test_dsh_filterbed -c tests/config/nextflow.config + tags: + - dsh + - dsh_filterbed + files: + - path: output/dsh/A.filtered.bed.gz + md5sum: 91cee4392d6034793f99f6c53891d866 \ No newline at end of file diff --git a/tests/software/dsh/splitbed/main.nf b/tests/software/dsh/splitbed/main.nf new file mode 100644 index 00000000..ed8286b9 --- /dev/null +++ b/tests/software/dsh/splitbed/main.nf @@ -0,0 +1,14 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { DSH_SPLITBED } from '../../../software/dsh/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] ) + +workflow test_dsh_splitbed { + + def input = [] + input = [ [ id:'A' ], // meta map + [ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ] + + DSH_SPLITBED ( input ) +} diff --git a/tests/software/dsh/splitbed/test.yml b/tests/software/dsh/splitbed/test.yml new file mode 100644 index 00000000..268cd463 --- /dev/null +++ b/tests/software/dsh/splitbed/test.yml @@ -0,0 +1,10 @@ +- name: dsh splitbed + command: nextflow run ./tests/software/dsh -entry test_dsh_splitbed -c tests/config/nextflow.config + tags: + - dsh + - dsh_splitbed + files: + - path: output/dsh/A.0.bed.gz + md5sum: 619e51c435d0e7138ca41b660ed07e3a + - path: output/dsh/A.1.bed.gz + md5sum: 223bba025a0bb859de9a1bf385550a7e diff --git a/tests/software/fastp/main.nf b/tests/software/fastp/main.nf index 000fcdd8..f035bc9c 100644 --- a/tests/software/fastp/main.nf +++ b/tests/software/fastp/main.nf @@ -7,24 +7,23 @@ include { FASTP } from '../../../software/fastp/main.nf' addParams( options: [: /* * Test with single-end data */ -workflow test_fastp_se { +workflow test_fastp_single_end { + def input = [] input = [ [ id:'test', single_end:true ], // meta map [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ] - - FASTP( input ) + FASTP ( input ) } /* * Test with paired-end data */ +workflow test_fastp_paired_end { -workflow test_fastp_pe { def input = [] input = [ [ id:'test', single_end:false ], // meta map [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] - - FASTP( input ) + FASTP ( input ) } diff --git a/tests/software/fastp/test.yml b/tests/software/fastp/test.yml index 5034c69a..b46c8dd7 100644 --- a/tests/software/fastp/test.yml +++ b/tests/software/fastp/test.yml @@ -1,8 +1,8 @@ -- name: fastp_se - command: nextflow run ./tests/software/fastp -entry test_fastp_se -c ./tests/config/nextflow.config +- name: fastp single-end + command: nextflow run ./tests/software/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config tags: - fastp - - fastp_se + - fastp_single_end files: - path: ./output/fastp/test.fastp.json md5sum: b81d53bfa5c1553bed89f6475edcf437 @@ -11,11 +11,11 @@ - path: ./output/fastp/test.fastp.log - path: ./output/fastp/test.fastp.html -- name: fastp_pe - command: nextflow run ./tests/software/fastp -entry test_fastp_pe -c ./tests/config/nextflow.config +- name: fastp paired-end + command: nextflow run ./tests/software/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config tags: - fastp - - fastp_pe + - fastp_paired_end files: - path: ./output/fastp/test.fastp.html - path: ./output/fastp/test.fastp.json diff --git a/tests/software/fastqc/main.nf b/tests/software/fastqc/main.nf index 27411a17..2ff1474a 100644 --- a/tests/software/fastqc/main.nf +++ b/tests/software/fastqc/main.nf @@ -2,35 +2,27 @@ nextflow.enable.dsl = 2 -include { FASTQC as FASTQC_SE } from '../../../software/fastqc/main.nf' addParams( options: [ publish_dir:'test_single_end' ] ) -include { FASTQC as FASTQC_PE } from '../../../software/fastqc/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] ) +include { FASTQC } from '../../../software/fastqc/main.nf' addParams( options: [:] ) /* * Test with single-end data */ -workflow test_single_end { +workflow test_fastqc_single_end { def input = [] input = [ [ id:'test', single_end:true ], // meta map [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ] - - FASTQC_SE ( input ) + FASTQC ( input ) } /* * Test with paired-end data */ -workflow test_paired_end { +workflow test_fastqc_paired_end { def input = [] input = [[id: 'test', single_end: false], // meta map [file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true)]] - - FASTQC_PE(input) - - emit: - html = FASTQC_PE.out.html - zip = FASTQC_PE.out.zip - + FASTQC (input) } diff --git a/tests/software/fastqc/test.yml b/tests/software/fastqc/test.yml index 2c0862dd..c883d599 100644 --- a/tests/software/fastqc/test.yml +++ b/tests/software/fastqc/test.yml @@ -1,15 +1,17 @@ -- name: Run fastqc single-end test workflow - command: nextflow run ./tests/software/fastqc/ -entry test_single_end -c tests/config/nextflow.config +- name: fastqc single-end + command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config tags: - fastqc + - fastqc_single_end files: - path: output/test_single_end/test_fastqc.html - path: output/test_single_end/test_fastqc.zip -- name: Run fastqc paired-end test workflow - command: nextflow run ./tests/software/fastqc/ -entry test_paired_end -c tests/config/nextflow.config +- name: fastqc paired-end + command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config tags: - fastqc + - fastqc_paired_end files: - path: output/test_paired_end/test_1_fastqc.html - path: output/test_paired_end/test_2_fastqc.html diff --git a/tests/software/gffread/test.yml b/tests/software/gffread/test.yml index a05e609d..d8547daa 100644 --- a/tests/software/gffread/test.yml +++ b/tests/software/gffread/test.yml @@ -1,4 +1,4 @@ -- name: Run gffread test workflow +- name: gffread command: nextflow run ./tests/software/gffread/ -entry test_gffread -c tests/config/nextflow.config tags: - gffread diff --git a/tests/software/multiqc/test.yml b/tests/software/multiqc/test.yml index 21dc36df..68df353d 100644 --- a/tests/software/multiqc/test.yml +++ b/tests/software/multiqc/test.yml @@ -1,4 +1,4 @@ -- name: Run multiqc test workflow +- name: multiqc command: nextflow run ./tests/software/multiqc/ -entry test_multiqc -c tests/config/nextflow.config tags: - multiqc diff --git a/tests/software/picard/collectmultiplemetrics/main.nf b/tests/software/picard/collectmultiplemetrics/main.nf new file mode 100644 index 00000000..423b10e1 --- /dev/null +++ b/tests/software/picard/collectmultiplemetrics/main.nf @@ -0,0 +1,17 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] ) + +workflow test_picard_collectmultiplemetrics { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ] + + PICARD_COLLECTMULTIPLEMETRICS ( + input, + file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + ) +} \ No newline at end of file diff --git a/tests/software/picard/collectmultiplemetrics/test.yml b/tests/software/picard/collectmultiplemetrics/test.yml new file mode 100644 index 00000000..0cda8949 --- /dev/null +++ b/tests/software/picard/collectmultiplemetrics/test.yml @@ -0,0 +1,16 @@ +- name: picard collectmultiplemetrics + command: nextflow run ./tests/software/picard -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config + tags: + - picard + - picard_collectmultiplemetrics + files: + # These can't be md5'd consistently + - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics + - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf + - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics + - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf + - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics + - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf + - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics + - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf + - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics \ No newline at end of file diff --git a/tests/software/picard/markduplicates/main.nf b/tests/software/picard/markduplicates/main.nf new file mode 100644 index 00000000..3b161b45 --- /dev/null +++ b/tests/software/picard/markduplicates/main.nf @@ -0,0 +1,23 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { PICARD_MARKDUPLICATES } from '../../../software/picard/markduplicates/main.nf' addParams( options: [:] ) + +workflow test_picard_markduplicates_sorted_bam { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + + PICARD_MARKDUPLICATES ( input ) +} + +workflow test_picard_markduplicates_unsorted_bam { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ] + + PICARD_MARKDUPLICATES ( input ) +} diff --git a/tests/software/picard/markduplicates/test.yml b/tests/software/picard/markduplicates/test.yml new file mode 100644 index 00000000..b9dfee34 --- /dev/null +++ b/tests/software/picard/markduplicates/test.yml @@ -0,0 +1,17 @@ +- name: picard markduplicates on sorted bam + command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config + tags: + - picard + - picard_markduplicates + files: + - path: output/picard/test.MarkDuplicates.metrics.txt + - path: output/picard/test.bam + md5sum: 0ed0bfc94069380334ccd595f6d8207c + +- name: picard markduplicates on unsorted bam + command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config + tags: + - picard + - picard_markduplicates + - should fail + exit_code: 1 diff --git a/tests/software/picard/mergesamfiles/main.nf b/tests/software/picard/mergesamfiles/main.nf new file mode 100644 index 00000000..1835c8ba --- /dev/null +++ b/tests/software/picard/mergesamfiles/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] ) + +workflow test_picard_mergesamfiles { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true), + file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true), ] ] + + PICARD_MERGESAMFILES ( input ) +} diff --git a/tests/software/picard/mergesamfiles/test.yml b/tests/software/picard/mergesamfiles/test.yml new file mode 100644 index 00000000..9273ff46 --- /dev/null +++ b/tests/software/picard/mergesamfiles/test.yml @@ -0,0 +1,8 @@ +- name: picard mergesamfiles + command: nextflow run ./tests/software/picard -entry test_picard_mergesamfiles -c tests/config/nextflow.config + tags: + - picard + - picard_mergesamfiles + files: + - path: output/picard/test.bam + md5sum: a9c8a28d1aac362df5973ba2d9923f86 \ No newline at end of file diff --git a/tests/software/preseq/lcextrap/main.nf b/tests/software/preseq/lcextrap/main.nf new file mode 100644 index 00000000..864e1230 --- /dev/null +++ b/tests/software/preseq/lcextrap/main.nf @@ -0,0 +1,29 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { PRESEQ_LCEXTRAP } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [:] ) + +/* + * Test with single-end data + */ +workflow test_preseq_single_end { + + def input = [] + input = [ [ id:'test', single_end:true ], // meta map + [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ] + PRESEQ_LCEXTRAP ( input ) +} + +/* + * Test with paired-end data + */ +workflow test_preseq_paired_end { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ] + + PRESEQ_LCEXTRAP ( input ) +} + diff --git a/tests/software/preseq/lcextrap/test.yml b/tests/software/preseq/lcextrap/test.yml new file mode 100644 index 00000000..51a7b08c --- /dev/null +++ b/tests/software/preseq/lcextrap/test.yml @@ -0,0 +1,21 @@ +- name: preseq lcextrap single-end + command: nextflow run ./tests/software/preseq -entry test_preseq_single_end -c tests/config/nextflow.config + tags: + - preseq + - preseq_lcextrap + - preseq_lcextrap_single_end + files: + - path: output/test_preseq_single_end/test.ccurve.txt + md5sum: 76ae04c8eaf19c94e3210bb69da38498 + - path: output/test_preseq_single_end/test.command.log + +- name: preseq lcextrap paired-end + command: nextflow run ./tests/software/preseq -entry test_preseq_paired_end -c tests/config/nextflow.config + tags: + - preseq + - preseq_lcextrap + - preseq_lcextrap_paired_end + files: + - path: output/test_preseq_paired_end/test.ccurve.txt + md5sum: 2836d2fabd2213f097fd7063db550276 + - path: output/test_preseq_paired_end/test.command.log diff --git a/tests/software/quast/test.yml b/tests/software/quast/test.yml index 17a7f056..43d909fd 100644 --- a/tests/software/quast/test.yml +++ b/tests/software/quast/test.yml @@ -1,4 +1,4 @@ -- name: quast_ref +- name: quast with reference command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config tags: - quast @@ -87,7 +87,7 @@ md5sum: d41d8cd98f00b204e9800998ecf8427e - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf -- name: quast_noref +- name: quast without reference command: nextflow run ./tests/software/quast -entry test_quast_noref -c ./tests/config/nextflow.config tags: - quast diff --git a/tests/software/salmon/index/main.nf b/tests/software/salmon/index/main.nf new file mode 100644 index 00000000..24fb76e2 --- /dev/null +++ b/tests/software/salmon/index/main.nf @@ -0,0 +1,11 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SALMON_INDEX } from '../../../software/salmon/index/main.nf' addParams( options: [args: '--minAssignedFrags 1'] ) + +workflow test_salmon_index { + def genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) + def transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true) + SALMON_INDEX ( genome_fasta, transcript_fasta ) +} \ No newline at end of file diff --git a/tests/software/salmon/index/test.yml b/tests/software/salmon/index/test.yml new file mode 100644 index 00000000..55bd848f --- /dev/null +++ b/tests/software/salmon/index/test.yml @@ -0,0 +1,31 @@ +- name: salmon index + command: nextflow run ./tests/software/salmon -entry test_salmon_index -c tests/config/nextflow.config + tags: + - salmon + - salmon_index + files: + - path: ./output/salmon/salmon/info.json + md5sum: 61ff4d3471134c280668355ddd39e99f + - path: ./output/salmon/salmon/mphf.bin + md5sum: 53669a47610e33e031faafd32703b714 + - path: ./output/salmon/salmon/complete_ref_lens.bin + md5sum: f57562f1fca3ae7b133f895ae13c3d08 + - path: ./output/salmon/salmon/ref_indexing.log + - path: ./output/salmon/salmon/versionInfo.json + md5sum: 204865f645102587c4953fccb256797c + - path: ./output/salmon/salmon/seq.bin + - path: ./output/salmon/salmon/pre_indexing.log + - path: ./output/salmon/salmon/rank.bin + md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71 + - path: ./output/salmon/salmon/reflengths.bin + md5sum: f57562f1fca3ae7b133f895ae13c3d08 + - path: ./output/salmon/salmon/ctable.bin + - path: ./output/salmon/salmon/ctg_offsets.bin + md5sum: 27a76542337df436436e66017f66dd25 + - path: ./output/salmon/salmon/pos.bin + - path: ./output/salmon/salmon/duplicate_clusters.tsv + md5sum: 51b5292e3a874119c0e1aa566e95d70c + - path: ./output/salmon/salmon/refAccumLengths.bin + md5sum: 8d1970505b2b08ca0eb5ff7722b48cde + - path: ./output/salmon/salmon/refseq.bin + md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7 \ No newline at end of file diff --git a/tests/software/salmon/quant/main.nf b/tests/software/salmon/quant/main.nf new file mode 100644 index 00000000..12e2792b --- /dev/null +++ b/tests/software/salmon/quant/main.nf @@ -0,0 +1,33 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SALMON_INDEX } from '../../../software/salmon/index/main.nf' addParams( options: [:] ) +include { SALMON_QUANT } from '../../../software/salmon/quant/main.nf' addParams( options: [args: '--minAssignedFrags 1'] ) + +workflow test_salmon_quant_single_end { + + def genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) + def transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true) + def gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true) + def input = [ [ id:'test', single_end:true ], // meta map + file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ] + + SALMON_INDEX ( genome_fasta, transcript_fasta ) + SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false) + +} + +workflow test_salmon_quant_paired_end { + + def genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) + def transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true) + def gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true) + def input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ] + + SALMON_INDEX ( genome_fasta, transcript_fasta ) + SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false) + +} \ No newline at end of file diff --git a/tests/software/salmon/quant/test.yml b/tests/software/salmon/quant/test.yml new file mode 100644 index 00000000..961e1171 --- /dev/null +++ b/tests/software/salmon/quant/test.yml @@ -0,0 +1,107 @@ +- name: salmon quant single-end + command: nextflow run ./tests/software/salmon -entry test_salmon_quant_single_end -c tests/config/nextflow.config + tags: + - salmon + - salmon_quant + - salmon_quant_single_end + files: + - path: ./output/salmon/salmon/versionInfo.json + md5sum: 204865f645102587c4953fccb256797c + - path: ./output/salmon/salmon/ctg_offsets.bin + md5sum: 27a76542337df436436e66017f66dd25 + - path: ./output/salmon/test/aux_info/meta_info.json + - path: ./output/salmon/salmon/duplicate_clusters.tsv + md5sum: 51b5292e3a874119c0e1aa566e95d70c + - path: ./output/salmon/salmon/pre_indexing.log + - path: ./output/salmon/salmon/rank.bin + md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71 + - path: ./output/salmon/test/aux_info/observed_bias.gz + md5sum: ef13c06a538e9c34ca9f84212c82f44e + - path: ./output/salmon/test/aux_info/expected_bias.gz + md5sum: 24ee10af39b41ecf4f4e08faaaf537ee + - path: ./output/salmon/test/aux_info/fld.gz + - path: ./output/salmon/salmon/ctable.bin + - path: ./output/salmon/salmon/info.json + md5sum: 61ff4d3471134c280668355ddd39e99f + - path: ./output/salmon/test/quant.genes.sf + md5sum: 5b39785b4d8da533c08ee4a6c8bc1211 + - path: ./output/salmon/salmon/refseq.bin + md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7 + - path: ./output/salmon/salmon/complete_ref_lens.bin + md5sum: f57562f1fca3ae7b133f895ae13c3d08 + - path: ./output/salmon/test/logs/salmon_quant.log + - path: ./output/salmon/test/libParams/flenDist.txt + md5sum: 2de170bdc9f6fd237d286429b292bb28 + - path: ./output/salmon/salmon/ref_indexing.log + - path: ./output/salmon/salmon/refAccumLengths.bin + md5sum: 8d1970505b2b08ca0eb5ff7722b48cde + - path: ./output/salmon/salmon/seq.bin + - path: ./output/salmon/salmon/mphf.bin + md5sum: 53669a47610e33e031faafd32703b714 + - path: ./output/salmon/test/aux_info/observed_bias_3p.gz + md5sum: ef13c06a538e9c34ca9f84212c82f44e + - path: ./output/salmon/test/lib_format_counts.json + md5sum: aca0a40187eb407b1b8fc85c01284583 + - path: ./output/salmon/salmon/reflengths.bin + md5sum: f57562f1fca3ae7b133f895ae13c3d08 + - path: ./output/salmon/salmon/pos.bin + - path: ./output/salmon/test/cmd_info.json + md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a + - path: ./output/salmon/test/aux_info/ambig_info.tsv + md5sum: c3306d26186ffe018ad4f19d52256180 + - path: ./output/salmon/test/quant.sf + md5sum: b08095ac70f89efc3146cdf488d0eb73 + +- name: salmon quant paired end + command: nextflow run ./tests/software/salmon -entry test_salmon_quant_paired_end -c tests/config/nextflow.config + tags: + - salmon + - salmon_quant + - salmon_quant_paired_end + files: + - path: ./output/salmon/salmon/pos.bin + - path: ./output/salmon/salmon/versionInfo.json + md5sum: 204865f645102587c4953fccb256797c + - path: ./output/salmon/salmon/complete_ref_lens.bin + md5sum: f57562f1fca3ae7b133f895ae13c3d08 + - path: ./output/salmon/test/lib_format_counts.json + md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea + - path: ./output/salmon/test/aux_info/expected_bias.gz + md5sum: 24ee10af39b41ecf4f4e08faaaf537ee + - path: ./output/salmon/test/libParams/flenDist.txt + md5sum: f90c7256c9b18d4131f4d4ecb69d0f55 + - path: ./output/salmon/salmon/ref_indexing.log + - path: ./output/salmon/test/aux_info/observed_bias_3p.gz + md5sum: ef13c06a538e9c34ca9f84212c82f44e + - path: ./output/salmon/salmon/ctable.bin + - path: ./output/salmon/test/aux_info/meta_info.json + - path: ./output/salmon/test/aux_info/fld.gz + - path: ./output/salmon/salmon/refseq.bin + md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7 + - path: ./output/salmon/salmon/info.json + md5sum: 61ff4d3471134c280668355ddd39e99f + - path: ./output/salmon/salmon/seq.bin + - path: ./output/salmon/test/cmd_info.json + md5sum: 007676e4d79de0809a03e0ea045ed4a1 + - path: ./output/salmon/test/aux_info/observed_bias.gz + md5sum: ef13c06a538e9c34ca9f84212c82f44e + - path: ./output/salmon/salmon/duplicate_clusters.tsv + md5sum: 51b5292e3a874119c0e1aa566e95d70c + - path: ./output/salmon/test/quant.genes.sf + md5sum: eb3e7b44801a0b3af07c25963927e20d + - path: ./output/salmon/salmon/rank.bin + md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71 + - path: ./output/salmon/salmon/mphf.bin + md5sum: 53669a47610e33e031faafd32703b714 + - path: ./output/salmon/test/aux_info/ambig_info.tsv + md5sum: 950001575c24fb6bc2c7a6848043b126 + - path: ./output/salmon/test/logs/salmon_quant.log + - path: ./output/salmon/salmon/pre_indexing.log + - path: ./output/salmon/salmon/refAccumLengths.bin + md5sum: 8d1970505b2b08ca0eb5ff7722b48cde + - path: ./output/salmon/test/quant.sf + md5sum: addb78e233f248b8f62cae3e217bf689 + - path: ./output/salmon/salmon/reflengths.bin + md5sum: f57562f1fca3ae7b133f895ae13c3d08 + - path: ./output/salmon/salmon/ctg_offsets.bin + md5sum: 27a76542337df436436e66017f66dd25 diff --git a/tests/software/samtools/flagstat/main.nf b/tests/software/samtools/flagstat/main.nf new file mode 100644 index 00000000..0d8a15b6 --- /dev/null +++ b/tests/software/samtools/flagstat/main.nf @@ -0,0 +1,14 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] ) + +workflow test_samtools_flagstat { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true), + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ] + SAMTOOLS_FLAGSTAT ( input ) +} \ No newline at end of file diff --git a/tests/software/samtools/flagstat/test.yml b/tests/software/samtools/flagstat/test.yml new file mode 100644 index 00000000..06f8ca9b --- /dev/null +++ b/tests/software/samtools/flagstat/test.yml @@ -0,0 +1,8 @@ +- name: samtools flagstat + command: nextflow run ./tests/software/samtools/ -entry test_samtools_flagstat -c tests/config/nextflow.config + tags: + - samtools + - samtools_flagstat + files: + - path: output/samtools/test.paired_end.sorted.bam.flagstat + md5sum: 80590621c74f5ee43ada20d010a3837f \ No newline at end of file diff --git a/tests/software/samtools/idxstats/main.nf b/tests/software/samtools/idxstats/main.nf new file mode 100644 index 00000000..aadb4465 --- /dev/null +++ b/tests/software/samtools/idxstats/main.nf @@ -0,0 +1,14 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] ) + +workflow test_samtools_idxstats { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true), + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ] + SAMTOOLS_IDXSTATS ( input ) +} \ No newline at end of file diff --git a/tests/software/samtools/idxstats/test.yml b/tests/software/samtools/idxstats/test.yml new file mode 100644 index 00000000..a1289a1b --- /dev/null +++ b/tests/software/samtools/idxstats/test.yml @@ -0,0 +1,8 @@ +- name: samtools idxstats + command: nextflow run ./tests/software/samtools/ -entry test_samtools_idxstats -c tests/config/nextflow.config + tags: + - samtools + - samtools_idxstats + files: + - path: output/samtools/test.paired_end.sorted.bam.idxstats + md5sum: 3bee8b7d55e412da2b3816c5a18d60d5 \ No newline at end of file diff --git a/tests/software/samtools/index/main.nf b/tests/software/samtools/index/main.nf new file mode 100644 index 00000000..181ae608 --- /dev/null +++ b/tests/software/samtools/index/main.nf @@ -0,0 +1,13 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] ) + +workflow test_samtools_index { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + SAMTOOLS_INDEX ( input ) +} diff --git a/tests/software/samtools/index/test.yml b/tests/software/samtools/index/test.yml new file mode 100644 index 00000000..52b5fd50 --- /dev/null +++ b/tests/software/samtools/index/test.yml @@ -0,0 +1,8 @@ +- name: samtools index + command: nextflow run ./tests/software/samtools/ -entry test_samtools_index -c tests/config/nextflow.config + tags: + - samtools + - samtools_index + files: + - path: output/samtools/test.paired_end.sorted.bam.bai + md5sum: 67338c2995eae82c849830ca55aa7bd1 \ No newline at end of file diff --git a/tests/software/samtools/mpileup/main.nf b/tests/software/samtools/mpileup/main.nf new file mode 100644 index 00000000..e84fb944 --- /dev/null +++ b/tests/software/samtools/mpileup/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SAMTOOLS_MPILEUP } from '../../../software/samtools/mpileup/main.nf' addParams( options: [:] ) + +workflow test_samtools_mpileup { + + def input = [] + def fasta = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ] + SAMTOOLS_MPILEUP ( input, fasta ) +} diff --git a/tests/software/samtools/mpileup/test.yml b/tests/software/samtools/mpileup/test.yml new file mode 100644 index 00000000..b1998c99 --- /dev/null +++ b/tests/software/samtools/mpileup/test.yml @@ -0,0 +1,8 @@ +- name: samtools mpileup + command: nextflow run ./tests/software/samtools/ -entry test_samtools_mpileup -c tests/config/nextflow.config + tags: + - samtools + - samtools_mpileup + files: + - path: output/samtools/test.mpileup + md5sum: 95c2646fa7bd535207722008c581c81d diff --git a/tests/software/samtools/sort/main.nf b/tests/software/samtools/sort/main.nf new file mode 100644 index 00000000..53c2a088 --- /dev/null +++ b/tests/software/samtools/sort/main.nf @@ -0,0 +1,13 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] ) + +workflow test_samtools_sort { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + SAMTOOLS_SORT ( input ) +} \ No newline at end of file diff --git a/tests/software/samtools/sort/test.yml b/tests/software/samtools/sort/test.yml new file mode 100644 index 00000000..7055f8bc --- /dev/null +++ b/tests/software/samtools/sort/test.yml @@ -0,0 +1,8 @@ +- name: samtools sort + command: nextflow run ./tests/software/samtools/ -entry test_samtools_sort -c tests/config/nextflow.config + tags: + - samtools + - samtools_sort + files: + - path: output/samtools/test.bam + md5sum: a41bfadacd2eeef1d31e05c135cc4f4e \ No newline at end of file diff --git a/tests/software/samtools/stats/main.nf b/tests/software/samtools/stats/main.nf new file mode 100644 index 00000000..f03fbd64 --- /dev/null +++ b/tests/software/samtools/stats/main.nf @@ -0,0 +1,14 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] ) + +workflow test_samtools_stats { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true), + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ] + SAMTOOLS_STATS ( input ) +} diff --git a/tests/software/samtools/stats/test.yml b/tests/software/samtools/stats/test.yml new file mode 100644 index 00000000..9295b258 --- /dev/null +++ b/tests/software/samtools/stats/test.yml @@ -0,0 +1,8 @@ +- name: samtools stats + command: nextflow run ./tests/software/samtools/ -entry test_samtools_stats -c tests/config/nextflow.config + tags: + - samtools + - samtools_stats + files: + - path: output/samtools/test.paired_end.sorted.bam.stats + md5sum: 06c183864d6e47ab89b0650cae831a93 \ No newline at end of file diff --git a/tests/software/samtools/view/main.nf b/tests/software/samtools/view/main.nf new file mode 100644 index 00000000..13c1fdf4 --- /dev/null +++ b/tests/software/samtools/view/main.nf @@ -0,0 +1,13 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: [:] ) + +workflow test_samtools_view { + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + SAMTOOLS_VIEW ( input ) +} \ No newline at end of file diff --git a/tests/software/samtools/view/test.yml b/tests/software/samtools/view/test.yml new file mode 100644 index 00000000..9ffabea4 --- /dev/null +++ b/tests/software/samtools/view/test.yml @@ -0,0 +1,8 @@ +- name: samtools view + command: nextflow run ./tests/software/samtools/ -entry test_samtools_view -c tests/config/nextflow.config + tags: + - samtools + - samtools_view + files: + - path: output/samtools/test.bam + md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff \ No newline at end of file diff --git a/tests/software/seacr/callpeak/main.nf b/tests/software/seacr/callpeak/main.nf new file mode 100644 index 00000000..9e4d9d9b --- /dev/null +++ b/tests/software/seacr/callpeak/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SEACR_CALLPEAK } from '../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] ) + +workflow test_seacr_callpeak { + + def input = [] + input = [[ id:'test_1'], + file("${launchDir}/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true), + file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ] + + SEACR_CALLPEAK ( input ) +} \ No newline at end of file diff --git a/tests/software/seacr/callpeak/test.yml b/tests/software/seacr/callpeak/test.yml new file mode 100644 index 00000000..6bdab27e --- /dev/null +++ b/tests/software/seacr/callpeak/test.yml @@ -0,0 +1,8 @@ +- name: seacr callpeak + command: nextflow run ./tests/software/seacr/ -entry test_seacr_callpeak -c tests/config/nextflow.config + tags: + - seacr + - seacr_callpeak + files: + - path: output/seacr/test_1.stringent.bed + md5sum: 3ac70475669eb6a7b8ca89e19a08a28e \ No newline at end of file diff --git a/tests/software/star/align/main.nf b/tests/software/star/align/main.nf new file mode 100644 index 00000000..1089c012 --- /dev/null +++ b/tests/software/star/align/main.nf @@ -0,0 +1,29 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] ) +include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] ) + +workflow test_star_alignment_single_end { + + def fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true) + def gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true) + STAR_GENOMEGENERATE ( fasta, gtf ) + + input = [ [ id:'test', single_end:true ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ] + STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf ) +} + +workflow test_star_alignment_paired_end { + + def fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true) + def gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true) + STAR_GENOMEGENERATE ( fasta, gtf ) + + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] + STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf ) +} diff --git a/tests/software/star/align/test.yml b/tests/software/star/align/test.yml new file mode 100644 index 00000000..00d25140 --- /dev/null +++ b/tests/software/star/align/test.yml @@ -0,0 +1,75 @@ +- name: star align single-end + command: nextflow run ./tests/software/star -entry test_star_alignment_single_end -c tests/config/nextflow.config + tags: + - star + - star_align + - star_align_single_end + files: + - path: output/star/star/Genome + md5sum: 323c992bac354f93073ce0fc43f222f8 + - path: output/star/star/SA + md5sum: 3e70e4fc6d031e1915bb510727f2c559 + - path: output/star/star/SAindex + md5sum: a94198b95a245d4f64af2a7133b6ec7b + - path: output/star/star/chrLength.txt + md5sum: f2bea3725fe1c01420c57fb73bdeb31a + - path: output/star/star/chrNameLength.txt + md5sum: c7ceb0a8827b2ea91c386933bee48742 + - path: output/star/star/chrStart.txt + md5sum: faf5c55020c99eceeef3e34188ac0d2f + - path: output/star/star/exonGeTrInfo.tab + md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 + - path: output/star/star/exonInfo.tab + md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 + - path: output/star/star/genomeParameters.txt + md5sum: ed47b8b034cae2fefcdb39321aea47cd + - path: output/star/star/sjdbInfo.txt + md5sum: 1082ab459363b3f2f7aabcef0979c1ed + - path: output/star/star/sjdbList.fromGTF.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/star/star/sjdbList.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/star/star/transcriptInfo.tab + md5sum: 8fbe69abbbef4f89da3854873984dbac + - path: output/star/test.Aligned.out.bam + md5sum: d7f59c1728482e76a18e3f6eb9c66c25 + - path: output/star/test.SJ.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + +- name: star align paired-end + command: nextflow run ./tests/software/star -entry test_star_alignment_paired_end -c tests/config/nextflow.config + tags: + - star + - star_align + - star_align_paired_end + files: + - path: output/star/star/Genome + md5sum: 323c992bac354f93073ce0fc43f222f8 + - path: output/star/star/SA + md5sum: 3e70e4fc6d031e1915bb510727f2c559 + - path: output/star/star/SAindex + md5sum: a94198b95a245d4f64af2a7133b6ec7b + - path: output/star/star/chrLength.txt + md5sum: f2bea3725fe1c01420c57fb73bdeb31a + - path: output/star/star/chrNameLength.txt + md5sum: c7ceb0a8827b2ea91c386933bee48742 + - path: output/star/star/chrStart.txt + md5sum: faf5c55020c99eceeef3e34188ac0d2f + - path: output/star/star/exonGeTrInfo.tab + md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 + - path: output/star/star/exonInfo.tab + md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 + - path: output/star/star/genomeParameters.txt + md5sum: ed47b8b034cae2fefcdb39321aea47cd + - path: output/star/star/sjdbInfo.txt + md5sum: 1082ab459363b3f2f7aabcef0979c1ed + - path: output/star/star/sjdbList.fromGTF.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/star/star/sjdbList.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/star/star/transcriptInfo.tab + md5sum: 8fbe69abbbef4f89da3854873984dbac + - path: output/star/test.Aligned.out.bam + md5sum: 5c52bcaa15e86914ad6b895638235166 + - path: output/star/test.SJ.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e diff --git a/tests/software/star/genomegenerate/main.nf b/tests/software/star/genomegenerate/main.nf new file mode 100644 index 00000000..c511ccd6 --- /dev/null +++ b/tests/software/star/genomegenerate/main.nf @@ -0,0 +1,12 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] ) + +workflow test_star_genomegenerate { + + def fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true) + def gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true) + STAR_GENOMEGENERATE ( fasta, gtf ) +} \ No newline at end of file diff --git a/tests/software/star/genomegenerate/test.yml b/tests/software/star/genomegenerate/test.yml new file mode 100644 index 00000000..e9533766 --- /dev/null +++ b/tests/software/star/genomegenerate/test.yml @@ -0,0 +1,32 @@ +- name: star genomegenerate + command: nextflow run ./tests/software/star -entry test_star_genomegenerate -c tests/config/nextflow.config + tags: + - star + - star_genomegenerate + files: + - path: output/star/star/Genome + md5sum: 323c992bac354f93073ce0fc43f222f8 + - path: output/star/star/SA + md5sum: 3e70e4fc6d031e1915bb510727f2c559 + - path: output/star/star/SAindex + md5sum: a94198b95a245d4f64af2a7133b6ec7b + - path: output/star/star/chrLength.txt + md5sum: f2bea3725fe1c01420c57fb73bdeb31a + - path: output/star/star/chrNameLength.txt + md5sum: c7ceb0a8827b2ea91c386933bee48742 + - path: output/star/star/chrStart.txt + md5sum: faf5c55020c99eceeef3e34188ac0d2f + - path: output/star/star/exonGeTrInfo.tab + md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 + - path: output/star/star/exonInfo.tab + md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 + - path: output/star/star/genomeParameters.txt + md5sum: ed47b8b034cae2fefcdb39321aea47cd + - path: output/star/star/sjdbInfo.txt + md5sum: 1082ab459363b3f2f7aabcef0979c1ed + - path: output/star/star/sjdbList.fromGTF.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/star/star/sjdbList.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/star/star/transcriptInfo.tab + md5sum: 8fbe69abbbef4f89da3854873984dbac \ No newline at end of file diff --git a/tests/software/stringtie/test.yml b/tests/software/stringtie/test.yml index 5bbf002b..f180d0c4 100644 --- a/tests/software/stringtie/test.yml +++ b/tests/software/stringtie/test.yml @@ -1,4 +1,4 @@ -- name: Run stringtie forward strand test workflow +- name: stringtie forward-strand command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_forward -c tests/config/nextflow.config tags: - stringtie @@ -20,7 +20,7 @@ - path: output/test_stringtie_forward/test.ballgown/t_data.ctab md5sum: 0106f70121a8b520d98b8739aed92915 -- name: Run stringtie reverse strand test workflow +- name: stringtie reverse-strand command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_reverse -c tests/config/nextflow.config tags: - stringtie diff --git a/tests/software/trimgalore/main.nf b/tests/software/trimgalore/main.nf index 0f03ee70..168805e8 100644 --- a/tests/software/trimgalore/main.nf +++ b/tests/software/trimgalore/main.nf @@ -2,8 +2,7 @@ nextflow.enable.dsl = 2 -include { TRIMGALORE as TRIMGALORE_SE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_single_end' ] ) -include { TRIMGALORE as TRIMGALORE_PE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] ) +include { TRIMGALORE } from '../../../software/trimgalore/main.nf' addParams( options: [:] ) /* * Test with single-end data @@ -13,19 +12,9 @@ workflow test_trimgalore_single_end { def input = [] input = [ [ id:'test', single_end:true ], // meta map [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ] - - TRIMGALORE_SE ( input ) + TRIMGALORE ( input ) } -// workflow test_trimgalore_single_end { - -// def input = [] -// input = [ [ id:'test', single_end:false ], // meta map -// [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ] - -// TRIMGALORE_SE ( input ) -// } - /* * Test with paired-end data */ @@ -36,5 +25,5 @@ workflow test_trimgalore_paired_end { [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] - TRIMGALORE_PE ( input ) + TRIMGALORE ( input ) } diff --git a/tests/software/trimgalore/test.yml b/tests/software/trimgalore/test.yml index 34d880db..a37ffdb6 100644 --- a/tests/software/trimgalore/test.yml +++ b/tests/software/trimgalore/test.yml @@ -1,4 +1,4 @@ -- name: Run trimgalore single-end test workflow +- name: trimgalore single-end command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_single_end -c tests/config/nextflow.config tags: - trimgalore @@ -8,7 +8,7 @@ - path: output/test_single_end/test.fastq.gz_trimming_report.txt - path: output/test_single_end/test_trimmed.fq.gz -- name: Run trimgalore paired-end test workflow +- name: trimgalore paired-end command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_paired_end -c tests/config/nextflow.config tags: - trimgalore diff --git a/tests/software/ucsc/bedgraphtobigwig/main.nf b/tests/software/ucsc/bedgraphtobigwig/main.nf new file mode 100644 index 00000000..deb13910 --- /dev/null +++ b/tests/software/ucsc/bedgraphtobigwig/main.nf @@ -0,0 +1,16 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { UCSC_BEDGRAPHTOBIGWIG } from '../../../software/ucsc/bedgraphtobigwig/main.nf' addParams( options: [:] ) + +workflow test_ucsc_bedgraphtobigwig { + def input = [] + input = [ [ id:'test' ], // meta map + [ file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/bedgraph-example-uscs.bedgraph', checkIfExists: true) ] ] + + UCSC_BEDGRAPHTOBIGWIG ( + input, + file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/chrom.sizes', checkIfExists: true) + ) +} diff --git a/tests/software/ucsc/bedgraphtobigwig/test.yml b/tests/software/ucsc/bedgraphtobigwig/test.yml new file mode 100644 index 00000000..d6052e6f --- /dev/null +++ b/tests/software/ucsc/bedgraphtobigwig/test.yml @@ -0,0 +1,7 @@ +- name: ucsc bedgraphtobigwig + command: nextflow run ./tests/software/ucsc/ -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config + tags: + - ucsc_bedgraphtobigwig + files: + - path: output/ucsc/test.bigWig + md5sum: 5346de25b01ecbff91b63178b3bfbeec From 743ba37d4ba3c6dd2b5edea3f238f167a2190d08 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 16:04:43 +0000 Subject: [PATCH 02/15] Update filters paths --- .github/filters.yml | 69 ++++++++------- tests/software/bowtie/main.nf | 33 -------- tests/software/bowtie/test.yml | 64 -------------- tests/software/bowtie2/main.nf | 33 -------- tests/software/bowtie2/test.yml | 64 -------------- tests/software/bwa/main.nf | 44 ---------- tests/software/bwa/test.yml | 32 ------- tests/software/dsh/main.nf | 24 ------ tests/software/dsh/test.yml | 19 ----- tests/software/picard/main.nf | 48 ----------- tests/software/picard/test.yml | 43 ---------- tests/software/preseq/main.nf | 32 ------- tests/software/preseq/test.yml | 21 ----- tests/software/salmon/main.nf | 35 -------- tests/software/salmon/test.yml | 139 ------------------------------- tests/software/samtools/main.nf | 80 ------------------ tests/software/samtools/test.yml | 62 -------------- tests/software/seacr/main.nf | 20 ----- tests/software/seacr/test.yml | 8 -- tests/software/star/main.nf | 36 -------- tests/software/star/test.yml | 108 ------------------------ tests/software/ucsc/main.nf | 15 ---- tests/software/ucsc/test.yml | 7 -- 23 files changed, 34 insertions(+), 1002 deletions(-) delete mode 100644 tests/software/bowtie/main.nf delete mode 100644 tests/software/bowtie/test.yml delete mode 100644 tests/software/bowtie2/main.nf delete mode 100644 tests/software/bowtie2/test.yml delete mode 100644 tests/software/bwa/main.nf delete mode 100644 tests/software/bwa/test.yml delete mode 100644 tests/software/dsh/main.nf delete mode 100644 tests/software/dsh/test.yml delete mode 100644 tests/software/picard/main.nf delete mode 100644 tests/software/picard/test.yml delete mode 100644 tests/software/preseq/main.nf delete mode 100644 tests/software/preseq/test.yml delete mode 100644 tests/software/salmon/main.nf delete mode 100644 tests/software/salmon/test.yml delete mode 100644 tests/software/samtools/main.nf delete mode 100644 tests/software/samtools/test.yml delete mode 100644 tests/software/seacr/main.nf delete mode 100644 tests/software/seacr/test.yml delete mode 100644 tests/software/star/main.nf delete mode 100644 tests/software/star/test.yml delete mode 100644 tests/software/ucsc/main.nf delete mode 100644 tests/software/ucsc/test.yml diff --git a/.github/filters.yml b/.github/filters.yml index 73f4637a..c0b8a9aa 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -1,28 +1,28 @@ -bowtie2_align: - - software/bowtie2/align/** - - software/bowtie2/build/** - - tests/software/bowtie2/** - -bowtie2_build: - - software/bowtie2/build/** - - tests/software/bowtie2/** - bowtie_align: - software/bowtie/align/** - software/bowtie/build/** - - tests/software/bowtie/** + - tests/software/bowtie/align/** bowtie_build: - software/bowtie/build/** - - tests/software/bowtie/** + - tests/software/bowtie/build/** + +bowtie2_align: + - software/bowtie2/align/** + - software/bowtie2/build/** + - tests/software/bowtie2/align/** + +bowtie2_build: + - software/bowtie2/build/** + - tests/software/bowtie2/build/** bwa_index: - software/bwa/index/** - - tests/software/bwa/** + - tests/software/bwa/index/** bwa_mem: - software/bwa/mem/** - - tests/software/bwa/** + - tests/software/bwa/mem/** cutadapt: - software/cutadapt/** @@ -30,11 +30,11 @@ cutadapt: dsh_filterbed: - software/dsh/filterbed/** - - tests/software/dsh/** + - tests/software/dsh/filterbed/** dsh_splitbed: - software/dsh/splitbed/** - - tests/software/dsh/** + - tests/software/dsh/splitbed/** fastp: - software/fastp/** @@ -58,19 +58,19 @@ pangolin: picard_collectmultiplemetrics: - software/picard/collectmultiplemetrics/** - - tests/software/picard/** + - tests/software/picard/collectmultiplemetrics/** picard_markduplicates: - software/picard/markduplicates/** - - tests/software/picard/** + - tests/software/picard/markduplicates/** picard_mergesamfiles: - software/picard/mergesamfiles/** - - tests/software/picard/** + - tests/software/picard/mergesamfiles/** preseq_lcextrap: - software/preseq/lcextrap/** - - tests/software/preseq/** + - tests/software/preseq/lcextrap/** quast: - software/quast/** @@ -78,56 +78,55 @@ quast: salmon_index: - software/salmon/index/** - - tests/software/salmon/** + - tests/software/salmon/index/** salmon_quant: - software/salmon/quant/** - - tests/software/salmon/** + - tests/software/salmon/quant/** samtools_flagstat: - software/samtools/flagstat/** - - tests/software/samtools/** + - tests/software/samtools/flagstat/** samtools_idxstats: - software/samtools/idxstats/** - - tests/software/samtools/** + - tests/software/samtools/idxstats/** samtools_index: - software/samtools/index/** - - tests/software/samtools/** + - tests/software/samtools/index/** samtools_mpileup: - software/samtools/mpileup/** - - tests/software/samtools/** + - tests/software/samtools/mpileup/** samtools_sort: - software/samtools/sort/** - - tests/software/samtools/** + - tests/software/samtools/sort/** samtools_stats: - software/samtools/stats/** - - tests/software/samtools/** + - tests/software/samtools/stats/** samtools_view: - software/samtools/view/** - - tests/software/samtools/** + - tests/software/samtools/view/** seacr_callpeak: - software/seacr/callpeak/** - - tests/software/seacr/** + - tests/software/seacr/callpeak/** star_align: - software/star/align/** - - tests/software/star/** + - tests/software/star/align/** star_genomegenerate: - software/star/genomegenerate/** - - tests/software/star/** - + - tests/software/star/genomegenerate/** stringtie: - - software/stringtie/** - - tests/software/stringtie/** + - software/stringtie/** + - tests/software/stringtie/** trimgalore: - software/trimgalore/** @@ -135,4 +134,4 @@ trimgalore: ucsc_bedgraphtobigwig: - software/ucsc/bedgraphtobigwig/** - - tests/software/ucsc/** + - tests/software/ucsc/bedgraphtobigwig/** diff --git a/tests/software/bowtie/main.nf b/tests/software/bowtie/main.nf deleted file mode 100644 index 1073195d..00000000 --- a/tests/software/bowtie/main.nf +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] ) -include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] ) - -workflow test_bowtie_build { - fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE_BUILD ( fasta ) -} - -workflow test_bowtie_alignment_single_end { - - fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE_BUILD ( fasta ) - - def input = [] - input = [ [ id:'test', single_end:true ], // meta map - [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ] - BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index ) -} - -workflow test_bowtie_alignment_paired_end { - fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE_BUILD ( fasta ) - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] - BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index ) -} diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml deleted file mode 100644 index 61ed5f1d..00000000 --- a/tests/software/bowtie/test.yml +++ /dev/null @@ -1,64 +0,0 @@ -- name: Run bowtie build - command: nextflow run ./tests/software/bowtie -entry test_bowtie_build -c tests/config/nextflow.config - tags: - - bowtie - - bowtie_build - files: - - path: output/bowtie/bowtie/NC_010473.1.ebwt - md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c - - path: output/bowtie/bowtie/NC_010473.2.ebwt - md5sum: bfd10c5319c6a0dbc540fd789254a5dd - - path: output/bowtie/bowtie/NC_010473.3.ebwt - md5sum: cd201e81724f3099131aec16ef2cc53b - - path: output/bowtie/bowtie/NC_010473.4.ebwt - md5sum: bbb9d6d21ad765d135f95290204e8433 - - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt - md5sum: 44f719c2fe42e1f35d54e798775846d1 - - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt - md5sum: f3c398bba5158f4039334a932d79c051 - -- name: Run bowtie build and align single-end - command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config - tags: - - bowtie - - bowtie_align - files: - - path: output/bowtie/bowtie/NC_010473.1.ebwt - md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c - - path: output/bowtie/bowtie/NC_010473.2.ebwt - md5sum: bfd10c5319c6a0dbc540fd789254a5dd - - path: output/bowtie/bowtie/NC_010473.3.ebwt - md5sum: cd201e81724f3099131aec16ef2cc53b - - path: output/bowtie/bowtie/NC_010473.4.ebwt - md5sum: bbb9d6d21ad765d135f95290204e8433 - - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt - md5sum: 44f719c2fe42e1f35d54e798775846d1 - - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt - md5sum: f3c398bba5158f4039334a932d79c051 - - path: output/bowtie/test.out - md5sum: a81cb18024616415a6cec3108a36fccd - - path: output/bowtie/test.bam - md5sum: 9feed8a55d4b5e600dcc577768ef07fc - -- name: Run bowtie index and align paired-end - command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config - tags: - - bowtie - - bowtie_align - files: - - path: output/bowtie/bowtie/NC_010473.1.ebwt - md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c - - path: output/bowtie/bowtie/NC_010473.2.ebwt - md5sum: bfd10c5319c6a0dbc540fd789254a5dd - - path: output/bowtie/bowtie/NC_010473.3.ebwt - md5sum: cd201e81724f3099131aec16ef2cc53b - - path: output/bowtie/bowtie/NC_010473.4.ebwt - md5sum: bbb9d6d21ad765d135f95290204e8433 - - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt - md5sum: 44f719c2fe42e1f35d54e798775846d1 - - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt - md5sum: f3c398bba5158f4039334a932d79c051 - - path: output/bowtie/test.out - md5sum: a23e9a2a76e949aeb3693bcfae41a615 - - path: output/bowtie/test.bam - md5sum: cf6a6381aa504e8342638ff3b509721e diff --git a/tests/software/bowtie2/main.nf b/tests/software/bowtie2/main.nf deleted file mode 100644 index a5a56cae..00000000 --- a/tests/software/bowtie2/main.nf +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] ) -include { BOWTIE2_ALIGN } from '../../../software/bowtie2/align/main.nf' addParams( options: [:] ) - -workflow test_bowtie2_build { - fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE2_BUILD ( fasta ) -} - -workflow test_bowtie2_alignment_single_end { - - fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE2_BUILD ( fasta ) - - def input = [] - input = [ [ id:'test', single_end:true ], // meta map - [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ] - BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index ) -} - -workflow test_bowtie2_alignment_paired_end { - fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE2_BUILD ( fasta ) - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] - BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index ) -} diff --git a/tests/software/bowtie2/test.yml b/tests/software/bowtie2/test.yml deleted file mode 100644 index f5ecbf12..00000000 --- a/tests/software/bowtie2/test.yml +++ /dev/null @@ -1,64 +0,0 @@ -- name: Run bowtie2 build - command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_build -c tests/config/nextflow.config - tags: - - bowtie2 - - bowtie2_build - files: - - path: output/bowtie2/bowtie2/NC_010473.1.bt2 - md5sum: 4db22d92e72111a5fbf609b3d9a43015 - - path: output/bowtie2/bowtie2/NC_010473.2.bt2 - md5sum: f4429ec74ee0064732c4bb26718a3eb1 - - path: output/bowtie2/bowtie2/NC_010473.3.bt2 - md5sum: cd201e81724f3099131aec16ef2cc53b - - path: output/bowtie2/bowtie2/NC_010473.4.bt2 - md5sum: bbb9d6d21ad765d135f95290204e8433 - - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 - md5sum: 4ccfee8857c3b1c69857e5ecdef597aa - - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 - md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 - -- name: Run bowtie2 index and align single-end - command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_alignment_single_end -c tests/config/nextflow.config - tags: - - bowtie2 - - bowtie2_align - files: - - path: output/bowtie2/bowtie2/NC_010473.1.bt2 - md5sum: 4db22d92e72111a5fbf609b3d9a43015 - - path: output/bowtie2/bowtie2/NC_010473.2.bt2 - md5sum: f4429ec74ee0064732c4bb26718a3eb1 - - path: output/bowtie2/bowtie2/NC_010473.3.bt2 - md5sum: cd201e81724f3099131aec16ef2cc53b - - path: output/bowtie2/bowtie2/NC_010473.4.bt2 - md5sum: bbb9d6d21ad765d135f95290204e8433 - - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 - md5sum: 4ccfee8857c3b1c69857e5ecdef597aa - - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 - md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 - - path: output/bowtie2/test.bowtie2.log - md5sum: 90041c264231be535042adb93a279356 - - path: output/bowtie2/test.bam - md5sum: 906102f401d8234b6473790988fb09cf - -- name: Run bowtie2 index and align paired-end - command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_alignment_paired_end -c tests/config/nextflow.config - tags: - - bowtie2 - - bowtie2_align - files: - - path: output/bowtie2/bowtie2/NC_010473.1.bt2 - md5sum: 4db22d92e72111a5fbf609b3d9a43015 - - path: output/bowtie2/bowtie2/NC_010473.2.bt2 - md5sum: f4429ec74ee0064732c4bb26718a3eb1 - - path: output/bowtie2/bowtie2/NC_010473.3.bt2 - md5sum: cd201e81724f3099131aec16ef2cc53b - - path: output/bowtie2/bowtie2/NC_010473.4.bt2 - md5sum: bbb9d6d21ad765d135f95290204e8433 - - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 - md5sum: 4ccfee8857c3b1c69857e5ecdef597aa - - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 - md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 - - path: output/bowtie2/test.bowtie2.log - md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5 - - path: output/bowtie2/test.bam - md5sum: 732a33cd9816b38ea9b919c25eeb78f8 diff --git a/tests/software/bwa/main.nf b/tests/software/bwa/main.nf deleted file mode 100644 index a4dcdbbf..00000000 --- a/tests/software/bwa/main.nf +++ /dev/null @@ -1,44 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] ) -include { BWA_MEM as BWA_MEM_SE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_single_end' ] ) -include { BWA_MEM as BWA_MEM_PE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] ) - -workflow test_bwa_index { - BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ) -} - -/* - * Test with single-end data - */ -workflow test_bwa_mem_single_end { - - def input = [] - input = [ [ id:'test', single_end:true ], // meta map - [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ] - - BWA_MEM_SE ( - input, - file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true), - file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - ) -} - -/* - * Test with paired-end data - */ -workflow test_bwa_mem_paired_end { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ] - - BWA_MEM_PE ( - input, - file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true), - file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - ) -} diff --git a/tests/software/bwa/test.yml b/tests/software/bwa/test.yml deleted file mode 100644 index 3258af5a..00000000 --- a/tests/software/bwa/test.yml +++ /dev/null @@ -1,32 +0,0 @@ -- name: Run bwa index - command: nextflow run ./tests/software/bwa -entry test_bwa_index -c tests/config/nextflow.config - tags: - - bwa - - bwa_index - files: - - path: output/bwa/NC_010473.fa.amb - md5sum: 942a990ae872f1c0b8d72dda2db405d5 - - path: output/bwa/NC_010473.fa.bwt - md5sum: 7301b52e2ecb893d429a49fa692447ae - - path: output/bwa/NC_010473.fa.pac - md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad - - path: output/bwa/NC_010473.fa.sa - md5sum: a47dcc92e750e2f16fbd979b8ff9538e - -- name: Run bwa mem single-end - command: nextflow run ./tests/software/bwa -entry test_bwa_mem_single_end -c tests/config/nextflow.config - tags: - - bwa - - bwa_mem - files: - - path: output/test_single_end/test.bam - md5sum: 3ee21210bac387e0335008146e4728bc - -- name: Run bwa mem paired-end - command: nextflow run ./tests/software/bwa -entry test_bwa_mem_paired_end -c tests/config/nextflow.config - tags: - - bwa - - bwa_mem - files: - - path: output/test_paired_end/test.bam - md5sum: 510d8acc6448c07cdacce8e64ec0904c diff --git a/tests/software/dsh/main.nf b/tests/software/dsh/main.nf deleted file mode 100644 index e007e3e1..00000000 --- a/tests/software/dsh/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { DSH_FILTERBED } from '../../../software/dsh/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] ) -include { DSH_SPLITBED } from '../../../software/dsh/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] ) - -workflow test_dsh_filterbed { - - def input = [] - input = [ [ id:'A' ], // meta map - [ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ] - - DSH_FILTERBED ( input ) -} - -workflow test_dsh_splitbed { - - def input = [] - input = [ [ id:'A' ], // meta map - [ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ] - - DSH_SPLITBED ( input ) -} diff --git a/tests/software/dsh/test.yml b/tests/software/dsh/test.yml deleted file mode 100644 index f58d2065..00000000 --- a/tests/software/dsh/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: Run dsh filterbed - command: nextflow run ./tests/software/dsh -entry test_dsh_filterbed -c tests/config/nextflow.config - tags: - - dsh - - dsh_filterbed - files: - - path: output/dsh/A.filtered.bed.gz - md5sum: 91cee4392d6034793f99f6c53891d866 - -- name: Run dsh splitbed - command: nextflow run ./tests/software/dsh -entry test_dsh_splitbed -c tests/config/nextflow.config - tags: - - dsh - - dsh_splitbed - files: - - path: output/dsh/A.0.bed.gz - md5sum: 619e51c435d0e7138ca41b660ed07e3a - - path: output/dsh/A.1.bed.gz - md5sum: 223bba025a0bb859de9a1bf385550a7e diff --git a/tests/software/picard/main.nf b/tests/software/picard/main.nf deleted file mode 100644 index d291de6d..00000000 --- a/tests/software/picard/main.nf +++ /dev/null @@ -1,48 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] ) -include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] ) -include { PICARD_MARKDUPLICATES } from '../../../software/picard/markduplicates/main.nf' addParams( options: [:] ) - -workflow test_picard_mergesamfiles { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true), - file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true), ] ] - - PICARD_MERGESAMFILES ( input ) -} - - -workflow test_picard_collectmultiplemetrics { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ] - - PICARD_COLLECTMULTIPLEMETRICS ( - input, - file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - ) -} - -workflow test_picard_markduplicates { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] - - PICARD_MARKDUPLICATES ( input ) -} - -workflow test_picard_markduplicates_not_sorted { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ] - - PICARD_MARKDUPLICATES ( input ) -} diff --git a/tests/software/picard/test.yml b/tests/software/picard/test.yml deleted file mode 100644 index 62554607..00000000 --- a/tests/software/picard/test.yml +++ /dev/null @@ -1,43 +0,0 @@ -- name: Run picard mergesamfiles - command: nextflow run ./tests/software/picard -entry test_picard_mergesamfiles -c tests/config/nextflow.config - tags: - - picard - - picard_mergesamfiles - files: - - path: output/picard/test.bam - md5sum: a9c8a28d1aac362df5973ba2d9923f86 - -- name: Run picard collectmultiplemetrics - command: nextflow run ./tests/software/picard -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config - tags: - - picard - - picard_collectmultiplemetrics - files: - # These can't be md5'd consistently - - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics - - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf - - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics - - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf - - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics - - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf - - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics - - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf - - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics - -- name: Run picard MarkDuplicates - command: nextflow run ./tests/software/picard -entry test_picard_markduplicates -c tests/config/nextflow.config - tags: - - picard - - picard_markduplicates - files: - - path: output/picard/test.MarkDuplicates.metrics.txt - - path: output/picard/test.bam - md5sum: 0ed0bfc94069380334ccd595f6d8207c - -- name: Run picard MarkDuplicates without a sorted bam file so it fails - command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config - tags: - - picard - - picard_markduplicates - - should fail - exit_code: 1 diff --git a/tests/software/preseq/main.nf b/tests/software/preseq/main.nf deleted file mode 100644 index 2091dcc6..00000000 --- a/tests/software/preseq/main.nf +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_SE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_single_end' ] ) -include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_PE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_paired_end' ] ) - -/* - * Test with single-end data - */ - -workflow test_preseq_single_end { - - def input = [] - input = [ [ id:'test', single_end:true ], // meta map - [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ] - PRESEQ_LCEXTRAP_SE ( input ) -} - -/* - * Test with paired-end data - */ - -workflow test_preseq_paired_end { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ] - - PRESEQ_LCEXTRAP_PE ( input ) -} - diff --git a/tests/software/preseq/test.yml b/tests/software/preseq/test.yml deleted file mode 100644 index 40eb6cdc..00000000 --- a/tests/software/preseq/test.yml +++ /dev/null @@ -1,21 +0,0 @@ -- name: Run preseq single-end lcextrap - command: nextflow run ./tests/software/preseq -entry test_preseq_single_end -c tests/config/nextflow.config - tags: - - preseq - - preseq_lcextrap - - files: - - path: output/test_preseq_single_end/test.ccurve.txt - md5sum: 76ae04c8eaf19c94e3210bb69da38498 - - path: output/test_preseq_single_end/test.command.log - -- name: Run preseq paired-end lcextrap - command: nextflow run ./tests/software/preseq -entry test_preseq_paired_end -c tests/config/nextflow.config - tags: - - preseq - - preseq_lcextrap - - files: - - path: output/test_preseq_paired_end/test.ccurve.txt - md5sum: 2836d2fabd2213f097fd7063db550276 - - path: output/test_preseq_paired_end/test.command.log diff --git a/tests/software/salmon/main.nf b/tests/software/salmon/main.nf deleted file mode 100644 index fe2ced56..00000000 --- a/tests/software/salmon/main.nf +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 -def quant_options = [args: '--minAssignedFrags 1'] -include { SALMON_INDEX } from '../../../software/salmon/index/main.nf' addParams( options: [:] ) -include { SALMON_QUANT } from '../../../software/salmon/quant/main.nf' addParams( options: quant_options ) - -workflow test_salmon_index { - genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) - transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true) - SALMON_INDEX ( genome_fasta, transcript_fasta ) -} - -workflow test_salmon_quant_pe { - genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) - transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true) - gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true) - input = [ [ id:'test', single_end:false ], // meta map - [ file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ] - - SALMON_INDEX ( genome_fasta, transcript_fasta ) - SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false) -} - -workflow test_salmon_quant_se { - genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) - transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true) - gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true) - input = [ [ id:'test', single_end:true ], // meta map - file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ] - - SALMON_INDEX ( genome_fasta, transcript_fasta ) - SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false) -} diff --git a/tests/software/salmon/test.yml b/tests/software/salmon/test.yml deleted file mode 100644 index 9febd8c1..00000000 --- a/tests/software/salmon/test.yml +++ /dev/null @@ -1,139 +0,0 @@ -- name: salmon index - command: nextflow run ./tests/software/salmon -entry test_salmon_index -c tests/config/nextflow.config - tags: - - salmon - - salmon_index - files: - - path: ./output/salmon/salmon/info.json - md5sum: 61ff4d3471134c280668355ddd39e99f - - path: ./output/salmon/salmon/mphf.bin - md5sum: 53669a47610e33e031faafd32703b714 - - path: ./output/salmon/salmon/complete_ref_lens.bin - md5sum: f57562f1fca3ae7b133f895ae13c3d08 - - path: ./output/salmon/salmon/ref_indexing.log - - path: ./output/salmon/salmon/versionInfo.json - md5sum: 204865f645102587c4953fccb256797c - - path: ./output/salmon/salmon/seq.bin - - path: ./output/salmon/salmon/pre_indexing.log - - path: ./output/salmon/salmon/rank.bin - md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71 - - path: ./output/salmon/salmon/reflengths.bin - md5sum: f57562f1fca3ae7b133f895ae13c3d08 - - path: ./output/salmon/salmon/ctable.bin - - path: ./output/salmon/salmon/ctg_offsets.bin - md5sum: 27a76542337df436436e66017f66dd25 - - path: ./output/salmon/salmon/pos.bin - - path: ./output/salmon/salmon/duplicate_clusters.tsv - md5sum: 51b5292e3a874119c0e1aa566e95d70c - - path: ./output/salmon/salmon/refAccumLengths.bin - md5sum: 8d1970505b2b08ca0eb5ff7722b48cde - - path: ./output/salmon/salmon/refseq.bin - md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7 - -- name: salmon quant paired end - command: nextflow run ./tests/software/salmon -entry test_salmon_quant_pe -c tests/config/nextflow.config - tags: - - salmon - - salmon_quant - - salmon_quant_pe - files: - - path: ./output/salmon/salmon/pos.bin - - path: ./output/salmon/salmon/versionInfo.json - md5sum: 204865f645102587c4953fccb256797c - - path: ./output/salmon/salmon/complete_ref_lens.bin - md5sum: f57562f1fca3ae7b133f895ae13c3d08 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea - - path: ./output/salmon/test/aux_info/expected_bias.gz - md5sum: 24ee10af39b41ecf4f4e08faaaf537ee - - path: ./output/salmon/test/libParams/flenDist.txt - md5sum: f90c7256c9b18d4131f4d4ecb69d0f55 - - path: ./output/salmon/salmon/ref_indexing.log - - path: ./output/salmon/test/aux_info/observed_bias_3p.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/salmon/ctable.bin - - path: ./output/salmon/test/aux_info/meta_info.json - - path: ./output/salmon/test/aux_info/fld.gz - - path: ./output/salmon/salmon/refseq.bin - md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7 - - path: ./output/salmon/salmon/info.json - md5sum: 61ff4d3471134c280668355ddd39e99f - - path: ./output/salmon/salmon/seq.bin - - path: ./output/salmon/test/cmd_info.json - md5sum: 007676e4d79de0809a03e0ea045ed4a1 - - path: ./output/salmon/test/aux_info/observed_bias.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/salmon/duplicate_clusters.tsv - md5sum: 51b5292e3a874119c0e1aa566e95d70c - - path: ./output/salmon/test/quant.genes.sf - md5sum: eb3e7b44801a0b3af07c25963927e20d - - path: ./output/salmon/salmon/rank.bin - md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71 - - path: ./output/salmon/salmon/mphf.bin - md5sum: 53669a47610e33e031faafd32703b714 - - path: ./output/salmon/test/aux_info/ambig_info.tsv - md5sum: 950001575c24fb6bc2c7a6848043b126 - - path: ./output/salmon/test/logs/salmon_quant.log - - path: ./output/salmon/salmon/pre_indexing.log - - path: ./output/salmon/salmon/refAccumLengths.bin - md5sum: 8d1970505b2b08ca0eb5ff7722b48cde - - path: ./output/salmon/test/quant.sf - md5sum: addb78e233f248b8f62cae3e217bf689 - - path: ./output/salmon/salmon/reflengths.bin - md5sum: f57562f1fca3ae7b133f895ae13c3d08 - - path: ./output/salmon/salmon/ctg_offsets.bin - md5sum: 27a76542337df436436e66017f66dd25 - -- name: salmon quant single-end - command: nextflow run ./tests/software/salmon -entry test_salmon_quant_se -c tests/config/nextflow.config - tags: - - salmon - - salmon_quant - - salmon_quant_se - files: - - path: ./output/salmon/salmon/versionInfo.json - md5sum: 204865f645102587c4953fccb256797c - - path: ./output/salmon/salmon/ctg_offsets.bin - md5sum: 27a76542337df436436e66017f66dd25 - - path: ./output/salmon/test/aux_info/meta_info.json - - path: ./output/salmon/salmon/duplicate_clusters.tsv - md5sum: 51b5292e3a874119c0e1aa566e95d70c - - path: ./output/salmon/salmon/pre_indexing.log - - path: ./output/salmon/salmon/rank.bin - md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71 - - path: ./output/salmon/test/aux_info/observed_bias.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/test/aux_info/expected_bias.gz - md5sum: 24ee10af39b41ecf4f4e08faaaf537ee - - path: ./output/salmon/test/aux_info/fld.gz - - path: ./output/salmon/salmon/ctable.bin - - path: ./output/salmon/salmon/info.json - md5sum: 61ff4d3471134c280668355ddd39e99f - - path: ./output/salmon/test/quant.genes.sf - md5sum: 5b39785b4d8da533c08ee4a6c8bc1211 - - path: ./output/salmon/salmon/refseq.bin - md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7 - - path: ./output/salmon/salmon/complete_ref_lens.bin - md5sum: f57562f1fca3ae7b133f895ae13c3d08 - - path: ./output/salmon/test/logs/salmon_quant.log - - path: ./output/salmon/test/libParams/flenDist.txt - md5sum: 2de170bdc9f6fd237d286429b292bb28 - - path: ./output/salmon/salmon/ref_indexing.log - - path: ./output/salmon/salmon/refAccumLengths.bin - md5sum: 8d1970505b2b08ca0eb5ff7722b48cde - - path: ./output/salmon/salmon/seq.bin - - path: ./output/salmon/salmon/mphf.bin - md5sum: 53669a47610e33e031faafd32703b714 - - path: ./output/salmon/test/aux_info/observed_bias_3p.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/salmon/reflengths.bin - md5sum: f57562f1fca3ae7b133f895ae13c3d08 - - path: ./output/salmon/salmon/pos.bin - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/aux_info/ambig_info.tsv - md5sum: c3306d26186ffe018ad4f19d52256180 - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 diff --git a/tests/software/samtools/main.nf b/tests/software/samtools/main.nf deleted file mode 100644 index bf96ae07..00000000 --- a/tests/software/samtools/main.nf +++ /dev/null @@ -1,80 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] ) -include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] ) -include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] ) -include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] ) -include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] ) -include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: [:] ) -include { SAMTOOLS_MPILEUP } from '../../../software/samtools/mpileup/main.nf' addParams( options: [:] ) - -workflow test_samtools_flagstat { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true), - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ] - - SAMTOOLS_FLAGSTAT ( input ) -} - -workflow test_samtools_idxstats { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true), - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ] - - SAMTOOLS_IDXSTATS ( input ) -} - -workflow test_samtools_index { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] - - SAMTOOLS_INDEX ( input ) -} - -// FIXME Why is this passing it an already sorted bam? -workflow test_samtools_sort { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] - - SAMTOOLS_SORT ( input ) -} - -workflow test_samtools_stats { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true), - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ] - - SAMTOOLS_STATS ( input ) -} - -workflow test_samtools_view { - - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] - - SAMTOOLS_VIEW ( input ) -} - -workflow test_samtools_mpileup { - - def input = [] - def fasta = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] - fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ] - - SAMTOOLS_MPILEUP ( input, fasta ) -} diff --git a/tests/software/samtools/test.yml b/tests/software/samtools/test.yml deleted file mode 100644 index c198cdd3..00000000 --- a/tests/software/samtools/test.yml +++ /dev/null @@ -1,62 +0,0 @@ -- name: Run samtools flagstat test workflow - command: nextflow run ./tests/software/samtools/ -entry test_samtools_flagstat -c tests/config/nextflow.config - tags: - - samtools - - samtools_flagstat - files: - - path: output/samtools/test.paired_end.sorted.bam.flagstat - md5sum: 80590621c74f5ee43ada20d010a3837f - -- name: Run samtools idxstats test workflow - command: nextflow run ./tests/software/samtools/ -entry test_samtools_idxstats -c tests/config/nextflow.config - tags: - - samtools - - samtools_idxstats - files: - - path: output/samtools/test.paired_end.sorted.bam.idxstats - md5sum: 3bee8b7d55e412da2b3816c5a18d60d5 - -- name: Run samtools index test workflow - command: nextflow run ./tests/software/samtools/ -entry test_samtools_index -c tests/config/nextflow.config - tags: - - samtools - - samtools_index - files: - - path: output/samtools/test.paired_end.sorted.bam.bai - md5sum: 67338c2995eae82c849830ca55aa7bd1 - -- name: Run samtools sort test workflow - command: nextflow run ./tests/software/samtools/ -entry test_samtools_sort -c tests/config/nextflow.config - tags: - - samtools - - samtools_sort - files: - - path: output/samtools/test.bam - md5sum: a41bfadacd2eeef1d31e05c135cc4f4e - -- name: Run samtools stats test workflow - command: nextflow run ./tests/software/samtools/ -entry test_samtools_stats -c tests/config/nextflow.config - tags: - - samtools - - samtools_stats - files: - - path: output/samtools/test.paired_end.sorted.bam.stats - md5sum: 06c183864d6e47ab89b0650cae831a93 - -- name: Run samtools view test workflow - command: nextflow run ./tests/software/samtools/ -entry test_samtools_view -c tests/config/nextflow.config - tags: - - samtools - - samtools_view - files: - - path: output/samtools/test.bam - md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff - -- name: Run samtools mpileup test workflow - command: nextflow run ./tests/software/samtools/ -entry test_samtools_mpileup -c tests/config/nextflow.config - tags: - - samtools - - samtools_mpileup - files: - - path: output/samtools/test.mpileup - md5sum: 95c2646fa7bd535207722008c581c81d diff --git a/tests/software/seacr/main.nf b/tests/software/seacr/main.nf deleted file mode 100644 index 7e3c4164..00000000 --- a/tests/software/seacr/main.nf +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { SEACR_CALLPEAK } from '../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] ) - -workflow test_seacr_callpeak { - - def input = [] - input = [[ id:'test_1'], - file("${launchDir}/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true), - file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ] - - SEACR_CALLPEAK ( input ) -} - -// For local testing -workflow { - test_seacr_callpeak() -} \ No newline at end of file diff --git a/tests/software/seacr/test.yml b/tests/software/seacr/test.yml deleted file mode 100644 index ed8306b1..00000000 --- a/tests/software/seacr/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: Run seacr call peak test workflow - command: nextflow run ./tests/software/seacr/ -entry test_seacr_callpeak -c tests/config/nextflow.config - tags: - - seacr - - seacr_callpeak - files: - - path: output/seacr/test_1.stringent.bed - md5sum: 3ac70475669eb6a7b8ca89e19a08a28e \ No newline at end of file diff --git a/tests/software/star/main.nf b/tests/software/star/main.nf deleted file mode 100644 index d6f1d6ee..00000000 --- a/tests/software/star/main.nf +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 -def options_align = [args: '--readFilesCommand zcat'] -def options_gg = [args: '--genomeSAindexNbases 9'] -include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: options_align ) -include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: options_gg ) - -workflow test_star_genomegenerate { - fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true) - gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true) - STAR_GENOMEGENERATE ( fasta, gtf ) -} - -workflow test_star_alignment_single_end { - fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true) - gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true) - STAR_GENOMEGENERATE ( fasta, gtf ) - - input = [ [ id:'test', single_end:true ], // meta map - [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ] - - STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf) -} - -workflow test_star_alignment_paired_end { - fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true) - gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true) - STAR_GENOMEGENERATE ( fasta, gtf ) - - input = [ [ id:'test', single_end:false ], // meta map - [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] - - STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf) -} diff --git a/tests/software/star/test.yml b/tests/software/star/test.yml deleted file mode 100644 index aca9595b..00000000 --- a/tests/software/star/test.yml +++ /dev/null @@ -1,108 +0,0 @@ -- name: Run star genomegenerate - command: nextflow run ./tests/software/star -entry test_star_genomegenerate -c tests/config/nextflow.config - tags: - - star - - star_genomegenerate - files: - - path: output/star/star/Genome - md5sum: 323c992bac354f93073ce0fc43f222f8 - - path: output/star/star/SA - md5sum: 3e70e4fc6d031e1915bb510727f2c559 - - path: output/star/star/SAindex - md5sum: a94198b95a245d4f64af2a7133b6ec7b - - path: output/star/star/chrLength.txt - md5sum: f2bea3725fe1c01420c57fb73bdeb31a - - path: output/star/star/chrNameLength.txt - md5sum: c7ceb0a8827b2ea91c386933bee48742 - - path: output/star/star/chrStart.txt - md5sum: faf5c55020c99eceeef3e34188ac0d2f - - path: output/star/star/exonGeTrInfo.tab - md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 - - path: output/star/star/exonInfo.tab - md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 - - path: output/star/star/genomeParameters.txt - md5sum: ed47b8b034cae2fefcdb39321aea47cd - - path: output/star/star/sjdbInfo.txt - md5sum: 1082ab459363b3f2f7aabcef0979c1ed - - path: output/star/star/sjdbList.fromGTF.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/star/star/sjdbList.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/star/star/transcriptInfo.tab - md5sum: 8fbe69abbbef4f89da3854873984dbac - -- name: Run star single-end alignment - command: nextflow run ./tests/software/star -entry test_star_alignment_single_end -c tests/config/nextflow.config - tags: - - star - - star_align - - star_alignment_single_end - files: - - path: output/star/star/Genome - md5sum: 323c992bac354f93073ce0fc43f222f8 - - path: output/star/star/SA - md5sum: 3e70e4fc6d031e1915bb510727f2c559 - - path: output/star/star/SAindex - md5sum: a94198b95a245d4f64af2a7133b6ec7b - - path: output/star/star/chrLength.txt - md5sum: f2bea3725fe1c01420c57fb73bdeb31a - - path: output/star/star/chrNameLength.txt - md5sum: c7ceb0a8827b2ea91c386933bee48742 - - path: output/star/star/chrStart.txt - md5sum: faf5c55020c99eceeef3e34188ac0d2f - - path: output/star/star/exonGeTrInfo.tab - md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 - - path: output/star/star/exonInfo.tab - md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 - - path: output/star/star/genomeParameters.txt - md5sum: ed47b8b034cae2fefcdb39321aea47cd - - path: output/star/star/sjdbInfo.txt - md5sum: 1082ab459363b3f2f7aabcef0979c1ed - - path: output/star/star/sjdbList.fromGTF.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/star/star/sjdbList.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/star/star/transcriptInfo.tab - md5sum: 8fbe69abbbef4f89da3854873984dbac - - path: output/star/test.Aligned.out.bam - md5sum: d7f59c1728482e76a18e3f6eb9c66c25 - - path: output/star/test.SJ.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - -- name: Run star paired-end alignment - command: nextflow run ./tests/software/star -entry test_star_alignment_paired_end -c tests/config/nextflow.config - tags: - - star - - star_align - - star_alignment_paired_end - files: - - path: output/star/star/Genome - md5sum: 323c992bac354f93073ce0fc43f222f8 - - path: output/star/star/SA - md5sum: 3e70e4fc6d031e1915bb510727f2c559 - - path: output/star/star/SAindex - md5sum: a94198b95a245d4f64af2a7133b6ec7b - - path: output/star/star/chrLength.txt - md5sum: f2bea3725fe1c01420c57fb73bdeb31a - - path: output/star/star/chrNameLength.txt - md5sum: c7ceb0a8827b2ea91c386933bee48742 - - path: output/star/star/chrStart.txt - md5sum: faf5c55020c99eceeef3e34188ac0d2f - - path: output/star/star/exonGeTrInfo.tab - md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 - - path: output/star/star/exonInfo.tab - md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 - - path: output/star/star/genomeParameters.txt - md5sum: ed47b8b034cae2fefcdb39321aea47cd - - path: output/star/star/sjdbInfo.txt - md5sum: 1082ab459363b3f2f7aabcef0979c1ed - - path: output/star/star/sjdbList.fromGTF.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/star/star/sjdbList.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/star/star/transcriptInfo.tab - md5sum: 8fbe69abbbef4f89da3854873984dbac - - path: output/star/test.Aligned.out.bam - md5sum: 5c52bcaa15e86914ad6b895638235166 - - path: output/star/test.SJ.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e diff --git a/tests/software/ucsc/main.nf b/tests/software/ucsc/main.nf deleted file mode 100644 index ce7df6b5..00000000 --- a/tests/software/ucsc/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { UCSC_BEDGRAPHTOBIGWIG } from '../../../software/ucsc/bedgraphtobigwig/main.nf' addParams( options: [:] ) - -workflow test_ucsc_bedgraphtobigwig { - def input = [] - input = [ [ id:'test' ], // meta map - [ file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/bedgraph-example-uscs.bedgraph', checkIfExists: true) ] ] - UCSC_BEDGRAPHTOBIGWIG ( - input, - file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/chrom.sizes', checkIfExists: true) - ) -} diff --git a/tests/software/ucsc/test.yml b/tests/software/ucsc/test.yml deleted file mode 100644 index fae05063..00000000 --- a/tests/software/ucsc/test.yml +++ /dev/null @@ -1,7 +0,0 @@ -- name: Run bedgraphtobigwig test workflow - command: nextflow run ./tests/software/ucsc/ -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config - tags: - - ucsc_bedgraphtobigwig - files: - - path: output/ucsc/test.bigWig - md5sum: 5346de25b01ecbff91b63178b3bfbeec From 239cbe17ad2a1c4fb72d60dcf6088ebb4e7466dc Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 16:20:02 +0000 Subject: [PATCH 03/15] Fix relative paths --- tests/software/bowtie/align/main.nf | 4 ++-- tests/software/bowtie/build/main.nf | 2 +- tests/software/bowtie2/align/main.nf | 4 ++-- tests/software/bowtie2/build/main.nf | 2 +- tests/software/bwa/index/main.nf | 2 +- tests/software/bwa/mem/main.nf | 2 +- tests/software/dsh/filterbed/main.nf | 2 +- tests/software/dsh/splitbed/main.nf | 2 +- tests/software/picard/collectmultiplemetrics/main.nf | 2 +- tests/software/picard/markduplicates/main.nf | 2 +- tests/software/picard/mergesamfiles/main.nf | 2 +- tests/software/preseq/lcextrap/main.nf | 2 +- tests/software/salmon/index/main.nf | 2 +- tests/software/salmon/quant/main.nf | 4 ++-- tests/software/samtools/flagstat/main.nf | 2 +- tests/software/samtools/idxstats/main.nf | 2 +- tests/software/samtools/index/main.nf | 2 +- tests/software/samtools/mpileup/main.nf | 2 +- tests/software/samtools/sort/main.nf | 2 +- tests/software/samtools/stats/main.nf | 2 +- tests/software/samtools/view/main.nf | 2 +- tests/software/seacr/callpeak/main.nf | 2 +- tests/software/star/align/main.nf | 4 ++-- tests/software/star/genomegenerate/main.nf | 2 +- tests/software/ucsc/bedgraphtobigwig/main.nf | 2 +- 25 files changed, 29 insertions(+), 29 deletions(-) diff --git a/tests/software/bowtie/align/main.nf b/tests/software/bowtie/align/main.nf index c31d5e2d..df12f79e 100644 --- a/tests/software/bowtie/align/main.nf +++ b/tests/software/bowtie/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] ) -include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] ) +include { BOWTIE_BUILD } from '../../../../software/bowtie/build/main.nf' addParams( options: [:] ) +include { BOWTIE_ALIGN } from '../../../../software/bowtie/align/main.nf' addParams( options: [:] ) workflow test_bowtie_alignment_single_end { diff --git a/tests/software/bowtie/build/main.nf b/tests/software/bowtie/build/main.nf index 4b43eb87..afe6e489 100644 --- a/tests/software/bowtie/build/main.nf +++ b/tests/software/bowtie/build/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] ) +include { BOWTIE_BUILD } from '../../../../software/bowtie/build/main.nf' addParams( options: [:] ) workflow test_bowtie_build { fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) diff --git a/tests/software/bowtie2/align/main.nf b/tests/software/bowtie2/align/main.nf index 89e9f250..a6d66555 100644 --- a/tests/software/bowtie2/align/main.nf +++ b/tests/software/bowtie2/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] ) -include { BOWTIE2_ALIGN } from '../../../software/bowtie2/align/main.nf' addParams( options: [:] ) +include { BOWTIE2_BUILD } from '../../../../software/bowtie2/build/main.nf' addParams( options: [:] ) +include { BOWTIE2_ALIGN } from '../../../../software/bowtie2/align/main.nf' addParams( options: [:] ) workflow test_bowtie2_align_single_end { diff --git a/tests/software/bowtie2/build/main.nf b/tests/software/bowtie2/build/main.nf index 9742d3ce..e760b0d1 100644 --- a/tests/software/bowtie2/build/main.nf +++ b/tests/software/bowtie2/build/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] ) +include { BOWTIE2_BUILD } from '../../../../software/bowtie2/build/main.nf' addParams( options: [:] ) workflow test_bowtie2_build { fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) diff --git a/tests/software/bwa/index/main.nf b/tests/software/bwa/index/main.nf index 93510a21..7da19f56 100644 --- a/tests/software/bwa/index/main.nf +++ b/tests/software/bwa/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] ) +include { BWA_INDEX } from '../../../../software/bwa/index/main.nf' addParams( options: [:] ) workflow test_bwa_index { BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ) diff --git a/tests/software/bwa/mem/main.nf b/tests/software/bwa/mem/main.nf index 0324546d..748b8e9f 100644 --- a/tests/software/bwa/mem/main.nf +++ b/tests/software/bwa/mem/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BWA_MEM } from '../../../software/bwa/mem/main.nf' addParams( options: [:] ) +include { BWA_MEM } from '../../../../software/bwa/mem/main.nf' addParams( options: [:] ) /* * Test with single-end data diff --git a/tests/software/dsh/filterbed/main.nf b/tests/software/dsh/filterbed/main.nf index f4d63496..98de8cac 100644 --- a/tests/software/dsh/filterbed/main.nf +++ b/tests/software/dsh/filterbed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSH_FILTERBED } from '../../../software/dsh/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] ) +include { DSH_FILTERBED } from '../../../../software/dsh/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] ) workflow test_dsh_filterbed { diff --git a/tests/software/dsh/splitbed/main.nf b/tests/software/dsh/splitbed/main.nf index ed8286b9..37cb41c7 100644 --- a/tests/software/dsh/splitbed/main.nf +++ b/tests/software/dsh/splitbed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSH_SPLITBED } from '../../../software/dsh/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] ) +include { DSH_SPLITBED } from '../../../../software/dsh/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] ) workflow test_dsh_splitbed { diff --git a/tests/software/picard/collectmultiplemetrics/main.nf b/tests/software/picard/collectmultiplemetrics/main.nf index 423b10e1..d53da770 100644 --- a/tests/software/picard/collectmultiplemetrics/main.nf +++ b/tests/software/picard/collectmultiplemetrics/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] ) +include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] ) workflow test_picard_collectmultiplemetrics { diff --git a/tests/software/picard/markduplicates/main.nf b/tests/software/picard/markduplicates/main.nf index 3b161b45..e8671965 100644 --- a/tests/software/picard/markduplicates/main.nf +++ b/tests/software/picard/markduplicates/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_MARKDUPLICATES } from '../../../software/picard/markduplicates/main.nf' addParams( options: [:] ) +include { PICARD_MARKDUPLICATES } from '../../../../software/picard/markduplicates/main.nf' addParams( options: [:] ) workflow test_picard_markduplicates_sorted_bam { diff --git a/tests/software/picard/mergesamfiles/main.nf b/tests/software/picard/mergesamfiles/main.nf index 1835c8ba..00ea3866 100644 --- a/tests/software/picard/mergesamfiles/main.nf +++ b/tests/software/picard/mergesamfiles/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] ) +include { PICARD_MERGESAMFILES } from '../../../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] ) workflow test_picard_mergesamfiles { diff --git a/tests/software/preseq/lcextrap/main.nf b/tests/software/preseq/lcextrap/main.nf index 864e1230..c15cd0bd 100644 --- a/tests/software/preseq/lcextrap/main.nf +++ b/tests/software/preseq/lcextrap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PRESEQ_LCEXTRAP } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [:] ) +include { PRESEQ_LCEXTRAP } from '../../../../software/preseq/lcextrap/main.nf' addParams( options: [:] ) /* * Test with single-end data diff --git a/tests/software/salmon/index/main.nf b/tests/software/salmon/index/main.nf index 24fb76e2..60dd102b 100644 --- a/tests/software/salmon/index/main.nf +++ b/tests/software/salmon/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SALMON_INDEX } from '../../../software/salmon/index/main.nf' addParams( options: [args: '--minAssignedFrags 1'] ) +include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addParams( options: [args: '--minAssignedFrags 1'] ) workflow test_salmon_index { def genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) diff --git a/tests/software/salmon/quant/main.nf b/tests/software/salmon/quant/main.nf index 12e2792b..bc973ed3 100644 --- a/tests/software/salmon/quant/main.nf +++ b/tests/software/salmon/quant/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SALMON_INDEX } from '../../../software/salmon/index/main.nf' addParams( options: [:] ) -include { SALMON_QUANT } from '../../../software/salmon/quant/main.nf' addParams( options: [args: '--minAssignedFrags 1'] ) +include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addParams( options: [:] ) +include { SALMON_QUANT } from '../../../../software/salmon/quant/main.nf' addParams( options: [args: '--minAssignedFrags 1'] ) workflow test_salmon_quant_single_end { diff --git a/tests/software/samtools/flagstat/main.nf b/tests/software/samtools/flagstat/main.nf index 0d8a15b6..7ca0b7e3 100644 --- a/tests/software/samtools/flagstat/main.nf +++ b/tests/software/samtools/flagstat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] ) +include { SAMTOOLS_FLAGSTAT } from '../../../../software/samtools/flagstat/main.nf' addParams( options: [:] ) workflow test_samtools_flagstat { diff --git a/tests/software/samtools/idxstats/main.nf b/tests/software/samtools/idxstats/main.nf index aadb4465..ca52f922 100644 --- a/tests/software/samtools/idxstats/main.nf +++ b/tests/software/samtools/idxstats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] ) +include { SAMTOOLS_IDXSTATS } from '../../../../software/samtools/idxstats/main.nf' addParams( options: [:] ) workflow test_samtools_idxstats { diff --git a/tests/software/samtools/index/main.nf b/tests/software/samtools/index/main.nf index 181ae608..1c93365e 100644 --- a/tests/software/samtools/index/main.nf +++ b/tests/software/samtools/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] ) +include { SAMTOOLS_INDEX } from '../../../../software/samtools/index/main.nf' addParams( options: [:] ) workflow test_samtools_index { diff --git a/tests/software/samtools/mpileup/main.nf b/tests/software/samtools/mpileup/main.nf index e84fb944..d09ad882 100644 --- a/tests/software/samtools/mpileup/main.nf +++ b/tests/software/samtools/mpileup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_MPILEUP } from '../../../software/samtools/mpileup/main.nf' addParams( options: [:] ) +include { SAMTOOLS_MPILEUP } from '../../../../software/samtools/mpileup/main.nf' addParams( options: [:] ) workflow test_samtools_mpileup { diff --git a/tests/software/samtools/sort/main.nf b/tests/software/samtools/sort/main.nf index 53c2a088..ab391bc9 100644 --- a/tests/software/samtools/sort/main.nf +++ b/tests/software/samtools/sort/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] ) +include { SAMTOOLS_SORT } from '../../../../software/samtools/sort/main.nf' addParams( options: [:] ) workflow test_samtools_sort { diff --git a/tests/software/samtools/stats/main.nf b/tests/software/samtools/stats/main.nf index f03fbd64..20c64ecb 100644 --- a/tests/software/samtools/stats/main.nf +++ b/tests/software/samtools/stats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] ) +include { SAMTOOLS_STATS } from '../../../../software/samtools/stats/main.nf' addParams( options: [:] ) workflow test_samtools_stats { diff --git a/tests/software/samtools/view/main.nf b/tests/software/samtools/view/main.nf index 13c1fdf4..610c9301 100644 --- a/tests/software/samtools/view/main.nf +++ b/tests/software/samtools/view/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: [:] ) +include { SAMTOOLS_VIEW } from '../../../../software/samtools/view/main.nf' addParams( options: [:] ) workflow test_samtools_view { diff --git a/tests/software/seacr/callpeak/main.nf b/tests/software/seacr/callpeak/main.nf index 9e4d9d9b..0fd734a7 100644 --- a/tests/software/seacr/callpeak/main.nf +++ b/tests/software/seacr/callpeak/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEACR_CALLPEAK } from '../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] ) +include { SEACR_CALLPEAK } from '../../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] ) workflow test_seacr_callpeak { diff --git a/tests/software/star/align/main.nf b/tests/software/star/align/main.nf index 1089c012..959dd0c8 100644 --- a/tests/software/star/align/main.nf +++ b/tests/software/star/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] ) -include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] ) +include { STAR_GENOMEGENERATE } from '../../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] ) +include { STAR_ALIGN } from '../../../../software/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] ) workflow test_star_alignment_single_end { diff --git a/tests/software/star/genomegenerate/main.nf b/tests/software/star/genomegenerate/main.nf index c511ccd6..d271e610 100644 --- a/tests/software/star/genomegenerate/main.nf +++ b/tests/software/star/genomegenerate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] ) +include { STAR_GENOMEGENERATE } from '../../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] ) workflow test_star_genomegenerate { diff --git a/tests/software/ucsc/bedgraphtobigwig/main.nf b/tests/software/ucsc/bedgraphtobigwig/main.nf index deb13910..c7af081f 100644 --- a/tests/software/ucsc/bedgraphtobigwig/main.nf +++ b/tests/software/ucsc/bedgraphtobigwig/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UCSC_BEDGRAPHTOBIGWIG } from '../../../software/ucsc/bedgraphtobigwig/main.nf' addParams( options: [:] ) +include { UCSC_BEDGRAPHTOBIGWIG } from '../../../../software/ucsc/bedgraphtobigwig/main.nf' addParams( options: [:] ) workflow test_ucsc_bedgraphtobigwig { def input = [] From 9b153f296d0a0347da5546e5e970b506c3f53939 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 16:26:10 +0000 Subject: [PATCH 04/15] Add check to see if bowtie bam files exists --- tests/software/bowtie/align/test.yml | 4 ++++ tests/software/bowtie2/align/test.yml | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml index 9356e1c7..eded71f2 100644 --- a/tests/software/bowtie/align/test.yml +++ b/tests/software/bowtie/align/test.yml @@ -19,6 +19,8 @@ md5sum: f3c398bba5158f4039334a932d79c051 - path: output/bowtie/test.out md5sum: a81cb18024616415a6cec3108a36fccd + - path: output/bowtie/test.bam + should_exist: true - name: bowtie align paired-end command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config @@ -41,3 +43,5 @@ md5sum: f3c398bba5158f4039334a932d79c051 - path: output/bowtie/test.out md5sum: a23e9a2a76e949aeb3693bcfae41a615 + - path: output/bowtie/test.bam + should_exist: true \ No newline at end of file diff --git a/tests/software/bowtie2/align/test.yml b/tests/software/bowtie2/align/test.yml index 43a702ee..fec516d6 100644 --- a/tests/software/bowtie2/align/test.yml +++ b/tests/software/bowtie2/align/test.yml @@ -18,6 +18,8 @@ md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 - path: output/bowtie2/test.bowtie2.log md5sum: 90041c264231be535042adb93a279356 + - path: output/bowtie2/test.bam + should_exist: true - name: bowtie2 align paired-end command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config @@ -39,3 +41,5 @@ md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 - path: output/bowtie2/test.bowtie2.log md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5 + - path: output/bowtie2/test.bam + should_exist: true \ No newline at end of file From a87d584c48f9c937ae9b36a20880babadb2d46ed Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 16:39:00 +0000 Subject: [PATCH 05/15] Change path to bowtie tests --- tests/software/bowtie/align/test.yml | 4 ++-- tests/software/bowtie/build/test.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml index eded71f2..4c12905f 100644 --- a/tests/software/bowtie/align/test.yml +++ b/tests/software/bowtie/align/test.yml @@ -1,5 +1,5 @@ - name: bowtie align single-end - command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config tags: - bowtie - bowtie_align @@ -23,7 +23,7 @@ should_exist: true - name: bowtie align paired-end - command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config tags: - bowtie - bowtie_align diff --git a/tests/software/bowtie/build/test.yml b/tests/software/bowtie/build/test.yml index 145836d6..4b8cfd7a 100644 --- a/tests/software/bowtie/build/test.yml +++ b/tests/software/bowtie/build/test.yml @@ -1,5 +1,5 @@ - name: bowtie build - command: nextflow run ./tests/software/bowtie -entry test_bowtie_build -c tests/config/nextflow.config + command: nextflow run ./tests/software/bowtie/build -entry test_bowtie_build -c tests/config/nextflow.config tags: - bowtie - bowtie_build From 305d47fc8772b7c3e4ab0f7f12870a2c9756bc71 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 16:44:56 +0000 Subject: [PATCH 06/15] Change path to tests --- tests/software/bowtie2/align/test.yml | 4 ++-- tests/software/bowtie2/build/test.yml | 2 +- tests/software/bwa/index/test.yml | 2 +- tests/software/bwa/mem/test.yml | 4 ++-- tests/software/dsh/filterbed/test.yml | 2 +- tests/software/dsh/splitbed/test.yml | 2 +- tests/software/picard/collectmultiplemetrics/test.yml | 2 +- tests/software/picard/markduplicates/test.yml | 4 ++-- tests/software/picard/mergesamfiles/test.yml | 2 +- tests/software/preseq/lcextrap/test.yml | 4 ++-- tests/software/salmon/index/test.yml | 2 +- tests/software/salmon/quant/test.yml | 2 +- tests/software/samtools/flagstat/test.yml | 2 +- tests/software/samtools/idxstats/test.yml | 2 +- tests/software/samtools/index/test.yml | 2 +- tests/software/samtools/mpileup/test.yml | 2 +- tests/software/samtools/sort/test.yml | 2 +- tests/software/samtools/stats/test.yml | 2 +- tests/software/samtools/view/test.yml | 2 +- tests/software/seacr/callpeak/test.yml | 2 +- tests/software/star/align/test.yml | 4 ++-- tests/software/star/genomegenerate/test.yml | 2 +- tests/software/ucsc/bedgraphtobigwig/test.yml | 2 +- 23 files changed, 28 insertions(+), 28 deletions(-) diff --git a/tests/software/bowtie2/align/test.yml b/tests/software/bowtie2/align/test.yml index fec516d6..52c51f3d 100644 --- a/tests/software/bowtie2/align/test.yml +++ b/tests/software/bowtie2/align/test.yml @@ -1,5 +1,5 @@ - name: bowtie2 align single-end - command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_align_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config tags: - bowtie2 - bowtie2_align_single_end @@ -22,7 +22,7 @@ should_exist: true - name: bowtie2 align paired-end - command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config tags: - bowtie2 - bowtie2_align_paired_end diff --git a/tests/software/bowtie2/build/test.yml b/tests/software/bowtie2/build/test.yml index 0c01844b..d172b5d2 100644 --- a/tests/software/bowtie2/build/test.yml +++ b/tests/software/bowtie2/build/test.yml @@ -1,5 +1,5 @@ - name: bowtie2 build - command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_build -c tests/config/nextflow.config + command: nextflow run ./tests/software/bowtie2/build -entry test_bowtie2_build -c tests/config/nextflow.config tags: - bowtie2 - bowtie2_build diff --git a/tests/software/bwa/index/test.yml b/tests/software/bwa/index/test.yml index 29d50d9b..89fe3f87 100644 --- a/tests/software/bwa/index/test.yml +++ b/tests/software/bwa/index/test.yml @@ -1,5 +1,5 @@ - name: bwa index - command: nextflow run ./tests/software/bwa -entry test_bwa_index -c tests/config/nextflow.config + command: nextflow run ./tests/software/bwa/index -entry test_bwa_index -c tests/config/nextflow.config tags: - bwa - bwa_index diff --git a/tests/software/bwa/mem/test.yml b/tests/software/bwa/mem/test.yml index 8c726066..9ce4ce50 100644 --- a/tests/software/bwa/mem/test.yml +++ b/tests/software/bwa/mem/test.yml @@ -1,5 +1,5 @@ - name: bwa mem single-end - command: nextflow run ./tests/software/bwa -entry test_bwa_mem_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_single_end -c tests/config/nextflow.config tags: - bwa - bwa_mem @@ -9,7 +9,7 @@ md5sum: 3ee21210bac387e0335008146e4728bc - name: bwa mem paired-end - command: nextflow run ./tests/software/bwa -entry test_bwa_mem_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_paired_end -c tests/config/nextflow.config tags: - bwa - bwa_mem diff --git a/tests/software/dsh/filterbed/test.yml b/tests/software/dsh/filterbed/test.yml index 989da517..aa4a6c3f 100644 --- a/tests/software/dsh/filterbed/test.yml +++ b/tests/software/dsh/filterbed/test.yml @@ -1,5 +1,5 @@ - name: dsh filterbed - command: nextflow run ./tests/software/dsh -entry test_dsh_filterbed -c tests/config/nextflow.config + command: nextflow run ./tests/software/dsh/filterbed -entry test_dsh_filterbed -c tests/config/nextflow.config tags: - dsh - dsh_filterbed diff --git a/tests/software/dsh/splitbed/test.yml b/tests/software/dsh/splitbed/test.yml index 268cd463..8bcbdd44 100644 --- a/tests/software/dsh/splitbed/test.yml +++ b/tests/software/dsh/splitbed/test.yml @@ -1,5 +1,5 @@ - name: dsh splitbed - command: nextflow run ./tests/software/dsh -entry test_dsh_splitbed -c tests/config/nextflow.config + command: nextflow run ./tests/software/dsh/splitbed -entry test_dsh_splitbed -c tests/config/nextflow.config tags: - dsh - dsh_splitbed diff --git a/tests/software/picard/collectmultiplemetrics/test.yml b/tests/software/picard/collectmultiplemetrics/test.yml index 0cda8949..78e4523d 100644 --- a/tests/software/picard/collectmultiplemetrics/test.yml +++ b/tests/software/picard/collectmultiplemetrics/test.yml @@ -1,5 +1,5 @@ - name: picard collectmultiplemetrics - command: nextflow run ./tests/software/picard -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config + command: nextflow run ./tests/software/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config tags: - picard - picard_collectmultiplemetrics diff --git a/tests/software/picard/markduplicates/test.yml b/tests/software/picard/markduplicates/test.yml index b9dfee34..c7c06a35 100644 --- a/tests/software/picard/markduplicates/test.yml +++ b/tests/software/picard/markduplicates/test.yml @@ -1,5 +1,5 @@ - name: picard markduplicates on sorted bam - command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config + command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config tags: - picard - picard_markduplicates @@ -9,7 +9,7 @@ md5sum: 0ed0bfc94069380334ccd595f6d8207c - name: picard markduplicates on unsorted bam - command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config + command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config tags: - picard - picard_markduplicates diff --git a/tests/software/picard/mergesamfiles/test.yml b/tests/software/picard/mergesamfiles/test.yml index 9273ff46..d2d77091 100644 --- a/tests/software/picard/mergesamfiles/test.yml +++ b/tests/software/picard/mergesamfiles/test.yml @@ -1,5 +1,5 @@ - name: picard mergesamfiles - command: nextflow run ./tests/software/picard -entry test_picard_mergesamfiles -c tests/config/nextflow.config + command: nextflow run ./tests/software/picard/mergesamfiles -entry test_picard_mergesamfiles -c tests/config/nextflow.config tags: - picard - picard_mergesamfiles diff --git a/tests/software/preseq/lcextrap/test.yml b/tests/software/preseq/lcextrap/test.yml index 51a7b08c..745effc7 100644 --- a/tests/software/preseq/lcextrap/test.yml +++ b/tests/software/preseq/lcextrap/test.yml @@ -1,5 +1,5 @@ - name: preseq lcextrap single-end - command: nextflow run ./tests/software/preseq -entry test_preseq_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_single_end -c tests/config/nextflow.config tags: - preseq - preseq_lcextrap @@ -10,7 +10,7 @@ - path: output/test_preseq_single_end/test.command.log - name: preseq lcextrap paired-end - command: nextflow run ./tests/software/preseq -entry test_preseq_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_paired_end -c tests/config/nextflow.config tags: - preseq - preseq_lcextrap diff --git a/tests/software/salmon/index/test.yml b/tests/software/salmon/index/test.yml index 55bd848f..f5ff4cc1 100644 --- a/tests/software/salmon/index/test.yml +++ b/tests/software/salmon/index/test.yml @@ -1,5 +1,5 @@ - name: salmon index - command: nextflow run ./tests/software/salmon -entry test_salmon_index -c tests/config/nextflow.config + command: nextflow run ./tests/software/salmon/index -entry test_salmon_index -c tests/config/nextflow.config tags: - salmon - salmon_index diff --git a/tests/software/salmon/quant/test.yml b/tests/software/salmon/quant/test.yml index 961e1171..a7ef3f5e 100644 --- a/tests/software/salmon/quant/test.yml +++ b/tests/software/salmon/quant/test.yml @@ -1,5 +1,5 @@ - name: salmon quant single-end - command: nextflow run ./tests/software/salmon -entry test_salmon_quant_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_single_end -c tests/config/nextflow.config tags: - salmon - salmon_quant diff --git a/tests/software/samtools/flagstat/test.yml b/tests/software/samtools/flagstat/test.yml index 06f8ca9b..2b2b197e 100644 --- a/tests/software/samtools/flagstat/test.yml +++ b/tests/software/samtools/flagstat/test.yml @@ -1,5 +1,5 @@ - name: samtools flagstat - command: nextflow run ./tests/software/samtools/ -entry test_samtools_flagstat -c tests/config/nextflow.config + command: nextflow run ./tests/software/samtools/flagstat -entry test_samtools_flagstat -c tests/config/nextflow.config tags: - samtools - samtools_flagstat diff --git a/tests/software/samtools/idxstats/test.yml b/tests/software/samtools/idxstats/test.yml index a1289a1b..6d62de25 100644 --- a/tests/software/samtools/idxstats/test.yml +++ b/tests/software/samtools/idxstats/test.yml @@ -1,5 +1,5 @@ - name: samtools idxstats - command: nextflow run ./tests/software/samtools/ -entry test_samtools_idxstats -c tests/config/nextflow.config + command: nextflow run ./tests/software/samtools/idxstats -entry test_samtools_idxstats -c tests/config/nextflow.config tags: - samtools - samtools_idxstats diff --git a/tests/software/samtools/index/test.yml b/tests/software/samtools/index/test.yml index 52b5fd50..7bc88142 100644 --- a/tests/software/samtools/index/test.yml +++ b/tests/software/samtools/index/test.yml @@ -1,5 +1,5 @@ - name: samtools index - command: nextflow run ./tests/software/samtools/ -entry test_samtools_index -c tests/config/nextflow.config + command: nextflow run ./tests/software/samtools/index -entry test_samtools_index -c tests/config/nextflow.config tags: - samtools - samtools_index diff --git a/tests/software/samtools/mpileup/test.yml b/tests/software/samtools/mpileup/test.yml index b1998c99..e2d31bc9 100644 --- a/tests/software/samtools/mpileup/test.yml +++ b/tests/software/samtools/mpileup/test.yml @@ -1,5 +1,5 @@ - name: samtools mpileup - command: nextflow run ./tests/software/samtools/ -entry test_samtools_mpileup -c tests/config/nextflow.config + command: nextflow run ./tests/software/samtools/mpileup -entry test_samtools_mpileup -c tests/config/nextflow.config tags: - samtools - samtools_mpileup diff --git a/tests/software/samtools/sort/test.yml b/tests/software/samtools/sort/test.yml index 7055f8bc..3b34ef25 100644 --- a/tests/software/samtools/sort/test.yml +++ b/tests/software/samtools/sort/test.yml @@ -1,5 +1,5 @@ - name: samtools sort - command: nextflow run ./tests/software/samtools/ -entry test_samtools_sort -c tests/config/nextflow.config + command: nextflow run ./tests/software/samtools/sort -entry test_samtools_sort -c tests/config/nextflow.config tags: - samtools - samtools_sort diff --git a/tests/software/samtools/stats/test.yml b/tests/software/samtools/stats/test.yml index 9295b258..d612e53d 100644 --- a/tests/software/samtools/stats/test.yml +++ b/tests/software/samtools/stats/test.yml @@ -1,5 +1,5 @@ - name: samtools stats - command: nextflow run ./tests/software/samtools/ -entry test_samtools_stats -c tests/config/nextflow.config + command: nextflow run ./tests/software/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config tags: - samtools - samtools_stats diff --git a/tests/software/samtools/view/test.yml b/tests/software/samtools/view/test.yml index 9ffabea4..6b793bdd 100644 --- a/tests/software/samtools/view/test.yml +++ b/tests/software/samtools/view/test.yml @@ -1,5 +1,5 @@ - name: samtools view - command: nextflow run ./tests/software/samtools/ -entry test_samtools_view -c tests/config/nextflow.config + command: nextflow run ./tests/software/samtools/view -entry test_samtools_view -c tests/config/nextflow.config tags: - samtools - samtools_view diff --git a/tests/software/seacr/callpeak/test.yml b/tests/software/seacr/callpeak/test.yml index 6bdab27e..e8e4bef0 100644 --- a/tests/software/seacr/callpeak/test.yml +++ b/tests/software/seacr/callpeak/test.yml @@ -1,5 +1,5 @@ - name: seacr callpeak - command: nextflow run ./tests/software/seacr/ -entry test_seacr_callpeak -c tests/config/nextflow.config + command: nextflow run ./tests/software/seacr/callpeak -entry test_seacr_callpeak -c tests/config/nextflow.config tags: - seacr - seacr_callpeak diff --git a/tests/software/star/align/test.yml b/tests/software/star/align/test.yml index 00d25140..7288aa14 100644 --- a/tests/software/star/align/test.yml +++ b/tests/software/star/align/test.yml @@ -1,5 +1,5 @@ - name: star align single-end - command: nextflow run ./tests/software/star -entry test_star_alignment_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/star/align -entry test_star_alignment_single_end -c tests/config/nextflow.config tags: - star - star_align @@ -37,7 +37,7 @@ md5sum: d41d8cd98f00b204e9800998ecf8427e - name: star align paired-end - command: nextflow run ./tests/software/star -entry test_star_alignment_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/star/align -entry test_star_alignment_paired_end -c tests/config/nextflow.config tags: - star - star_align diff --git a/tests/software/star/genomegenerate/test.yml b/tests/software/star/genomegenerate/test.yml index e9533766..27d21ad5 100644 --- a/tests/software/star/genomegenerate/test.yml +++ b/tests/software/star/genomegenerate/test.yml @@ -1,5 +1,5 @@ - name: star genomegenerate - command: nextflow run ./tests/software/star -entry test_star_genomegenerate -c tests/config/nextflow.config + command: nextflow run ./tests/software/star/genomegenerate -entry test_star_genomegenerate -c tests/config/nextflow.config tags: - star - star_genomegenerate diff --git a/tests/software/ucsc/bedgraphtobigwig/test.yml b/tests/software/ucsc/bedgraphtobigwig/test.yml index d6052e6f..43ebc22c 100644 --- a/tests/software/ucsc/bedgraphtobigwig/test.yml +++ b/tests/software/ucsc/bedgraphtobigwig/test.yml @@ -1,5 +1,5 @@ - name: ucsc bedgraphtobigwig - command: nextflow run ./tests/software/ucsc/ -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config + command: nextflow run ./tests/software/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config tags: - ucsc_bedgraphtobigwig files: From 39b8600dbbec6e193314c410c81931427908a9a8 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 17:02:52 +0000 Subject: [PATCH 07/15] Fix trimgalore test --- tests/software/trimgalore/test.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/software/trimgalore/test.yml b/tests/software/trimgalore/test.yml index a37ffdb6..a3fba07b 100644 --- a/tests/software/trimgalore/test.yml +++ b/tests/software/trimgalore/test.yml @@ -5,8 +5,8 @@ files: # These can't be md5'd reliably # TODO Test for includes - - path: output/test_single_end/test.fastq.gz_trimming_report.txt - - path: output/test_single_end/test_trimmed.fq.gz + - path: output/trimgalore/test.fastq.gz_trimming_report.txt + - path: output/trimgalore/test_trimmed.fq.gz - name: trimgalore paired-end command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_paired_end -c tests/config/nextflow.config @@ -15,7 +15,7 @@ files: # These can't be md5'd reliably # TODO Test for includes - - path: output/test_paired_end/test_1.fastq.gz_trimming_report.txt - - path: output/test_paired_end/test_1_val_1.fq.gz - - path: output/test_paired_end/test_2.fastq.gz_trimming_report.txt - - path: output/test_paired_end/test_2_val_2.fq.gz + - path: output/trimgalore/test_1.fastq.gz_trimming_report.txt + - path: output/trimgalore/test_1_val_1.fq.gz + - path: output/trimgalore/test_2.fastq.gz_trimming_report.txt + - path: output/trimgalore/test_2_val_2.fq.gz From 058d7b397cce3b6700d1f9da0a3f3661689d4790 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 17:03:30 +0000 Subject: [PATCH 08/15] Fix fastqc test --- tests/software/fastqc/test.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/software/fastqc/test.yml b/tests/software/fastqc/test.yml index c883d599..7590cd44 100644 --- a/tests/software/fastqc/test.yml +++ b/tests/software/fastqc/test.yml @@ -4,8 +4,8 @@ - fastqc - fastqc_single_end files: - - path: output/test_single_end/test_fastqc.html - - path: output/test_single_end/test_fastqc.zip + - path: output/fastqc/test_fastqc.html + - path: output/fastqc/test_fastqc.zip - name: fastqc paired-end command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config @@ -13,7 +13,7 @@ - fastqc - fastqc_paired_end files: - - path: output/test_paired_end/test_1_fastqc.html - - path: output/test_paired_end/test_2_fastqc.html - - path: output/test_paired_end/test_1_fastqc.zip - - path: output/test_paired_end/test_2_fastqc.zip + - path: output/fastqc/test_1_fastqc.html + - path: output/fastqc/test_2_fastqc.html + - path: output/fastqc/test_1_fastqc.zip + - path: output/fastqc/test_2_fastqc.zip From 8a15852756ae26f778f130e7012f4c7545436630 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 17:13:47 +0000 Subject: [PATCH 09/15] Fix salmon index tests --- tests/software/salmon/index/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/software/salmon/index/main.nf b/tests/software/salmon/index/main.nf index 60dd102b..792f8cdf 100644 --- a/tests/software/salmon/index/main.nf +++ b/tests/software/salmon/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addParams( options: [args: '--minAssignedFrags 1'] ) +include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addParams( options: [:] ) workflow test_salmon_index { def genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) From f37fb66f40903672ce8a26d3abf17f0a306822df Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 17:26:43 +0000 Subject: [PATCH 10/15] Fix bwa mem tests --- tests/software/bwa/mem/test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/software/bwa/mem/test.yml b/tests/software/bwa/mem/test.yml index 9ce4ce50..decf2e44 100644 --- a/tests/software/bwa/mem/test.yml +++ b/tests/software/bwa/mem/test.yml @@ -5,7 +5,7 @@ - bwa_mem - bwa_mem_single_end files: - - path: output/test_single_end/test.bam + - path: output/bwa/test.bam md5sum: 3ee21210bac387e0335008146e4728bc - name: bwa mem paired-end @@ -15,5 +15,5 @@ - bwa_mem - bwa_mem_paired_end files: - - path: output/test_paired_end/test.bam + - path: output/bwa/test.bam md5sum: 510d8acc6448c07cdacce8e64ec0904c From f079ce9d1fa5e655320274e829b2d4a36572b1f7 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 17:28:44 +0000 Subject: [PATCH 11/15] Fix preseq tests --- tests/software/preseq/lcextrap/test.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/software/preseq/lcextrap/test.yml b/tests/software/preseq/lcextrap/test.yml index 745effc7..7e1552f7 100644 --- a/tests/software/preseq/lcextrap/test.yml +++ b/tests/software/preseq/lcextrap/test.yml @@ -5,9 +5,9 @@ - preseq_lcextrap - preseq_lcextrap_single_end files: - - path: output/test_preseq_single_end/test.ccurve.txt + - path: output/preseq/test.ccurve.txt md5sum: 76ae04c8eaf19c94e3210bb69da38498 - - path: output/test_preseq_single_end/test.command.log + - path: output/preseq/test.command.log - name: preseq lcextrap paired-end command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_paired_end -c tests/config/nextflow.config @@ -16,6 +16,6 @@ - preseq_lcextrap - preseq_lcextrap_paired_end files: - - path: output/test_preseq_paired_end/test.ccurve.txt + - path: output/preseq/test.ccurve.txt md5sum: 2836d2fabd2213f097fd7063db550276 - - path: output/test_preseq_paired_end/test.command.log + - path: output/preseq/test.command.log From 550494cbd10ab6722aa6f8e6b43e71973eab8d66 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 17:31:41 +0000 Subject: [PATCH 12/15] Fix picard mergesamfiles test --- tests/software/picard/mergesamfiles/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/software/picard/mergesamfiles/main.nf b/tests/software/picard/mergesamfiles/main.nf index 00ea3866..cedbbecb 100644 --- a/tests/software/picard/mergesamfiles/main.nf +++ b/tests/software/picard/mergesamfiles/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_MERGESAMFILES } from '../../../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] ) +include { PICARD_MERGESAMFILES } from '../../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] ) workflow test_picard_mergesamfiles { From 0683efc67929856c1029d247f55f283cf6f1e1c1 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 17:36:06 +0000 Subject: [PATCH 13/15] Fix salmon quant tests --- tests/software/salmon/quant/main.nf | 4 ++-- tests/software/salmon/quant/test.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/software/salmon/quant/main.nf b/tests/software/salmon/quant/main.nf index bc973ed3..7ee8a047 100644 --- a/tests/software/salmon/quant/main.nf +++ b/tests/software/salmon/quant/main.nf @@ -14,7 +14,7 @@ workflow test_salmon_quant_single_end { file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ] SALMON_INDEX ( genome_fasta, transcript_fasta ) - SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false) + SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false ) } @@ -28,6 +28,6 @@ workflow test_salmon_quant_paired_end { file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ] SALMON_INDEX ( genome_fasta, transcript_fasta ) - SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false) + SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false ) } \ No newline at end of file diff --git a/tests/software/salmon/quant/test.yml b/tests/software/salmon/quant/test.yml index a7ef3f5e..021abdf3 100644 --- a/tests/software/salmon/quant/test.yml +++ b/tests/software/salmon/quant/test.yml @@ -53,7 +53,7 @@ md5sum: b08095ac70f89efc3146cdf488d0eb73 - name: salmon quant paired end - command: nextflow run ./tests/software/salmon -entry test_salmon_quant_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_paired_end -c tests/config/nextflow.config tags: - salmon - salmon_quant From ff6f0642d29e80864895bd1e50e8c3d7ce0fd56d Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 17:43:14 +0000 Subject: [PATCH 14/15] Fix multiqc tests --- .github/filters.yml | 1 + tests/software/multiqc/main.nf | 18 +++++++++--------- tests/software/multiqc/test.yml | 4 ++-- 3 files changed, 12 insertions(+), 11 deletions(-) diff --git a/.github/filters.yml b/.github/filters.yml index c0b8a9aa..8bdb79be 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -49,6 +49,7 @@ gffread: - tests/software/gffread/** multiqc: + - software/fastqc/** - software/multiqc/** - tests/software/multiqc/** diff --git a/tests/software/multiqc/main.nf b/tests/software/multiqc/main.nf index 06b466ab..9d7ec3aa 100644 --- a/tests/software/multiqc/main.nf +++ b/tests/software/multiqc/main.nf @@ -2,15 +2,15 @@ nextflow.enable.dsl = 2 -include { MULTIQC } from '../../../software/multiqc/main.nf' addParams(options: [publish_dir: 'test_multiqc']) -include { test_paired_end } from '../fastqc/main.nf' addParams(options: [publish_dir: 'test_paired_end']) +include { FASTQC } from '../../../software/fastqc/main.nf' addParams( options: [:] ) +include { MULTIQC } from '../../../software/multiqc/main.nf' addParams( options: [:] ) workflow test_multiqc { - test_paired_end() - - input = [ - test_paired_end.out.zip.collect { it[1] }.ifEmpty([]) - ] - - MULTIQC(*input) + + def input = [] + input = [ [ id: 'test', single_end: false ], + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] + FASTQC ( input ) + MULTIQC ( FASTQC.out.zip.collect { it[1] } ) } diff --git a/tests/software/multiqc/test.yml b/tests/software/multiqc/test.yml index 68df353d..72ce58f1 100644 --- a/tests/software/multiqc/test.yml +++ b/tests/software/multiqc/test.yml @@ -1,7 +1,7 @@ - name: multiqc - command: nextflow run ./tests/software/multiqc/ -entry test_multiqc -c tests/config/nextflow.config + command: nextflow run ./tests/software/multiqc -entry test_multiqc -c tests/config/nextflow.config tags: - multiqc files: - - path: output/test_multiqc/multiqc_report.html + - path: output/multiqc/multiqc_report.html From e71b3eaaa544d026d47b97a90f72c662817c8117 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 17:48:17 +0000 Subject: [PATCH 15/15] Rename workflows --- tests/software/bowtie/align/main.nf | 4 ++-- tests/software/bowtie/align/test.yml | 4 ++-- tests/software/bowtie2/align/test.yml | 2 ++ 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/tests/software/bowtie/align/main.nf b/tests/software/bowtie/align/main.nf index df12f79e..d3dfa500 100644 --- a/tests/software/bowtie/align/main.nf +++ b/tests/software/bowtie/align/main.nf @@ -5,7 +5,7 @@ nextflow.enable.dsl = 2 include { BOWTIE_BUILD } from '../../../../software/bowtie/build/main.nf' addParams( options: [:] ) include { BOWTIE_ALIGN } from '../../../../software/bowtie/align/main.nf' addParams( options: [:] ) -workflow test_bowtie_alignment_single_end { +workflow test_bowtie_align_single_end { def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) BOWTIE_BUILD ( fasta ) @@ -16,7 +16,7 @@ workflow test_bowtie_alignment_single_end { BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index ) } -workflow test_bowtie_alignment_paired_end { +workflow test_bowtie_align_paired_end { def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) BOWTIE_BUILD ( fasta ) diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml index 4c12905f..a941b233 100644 --- a/tests/software/bowtie/align/test.yml +++ b/tests/software/bowtie/align/test.yml @@ -1,5 +1,5 @@ - name: bowtie align single-end - command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_align_single_end -c tests/config/nextflow.config tags: - bowtie - bowtie_align @@ -23,7 +23,7 @@ should_exist: true - name: bowtie align paired-end - command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_align_single_end -c tests/config/nextflow.config tags: - bowtie - bowtie_align diff --git a/tests/software/bowtie2/align/test.yml b/tests/software/bowtie2/align/test.yml index 52c51f3d..49266c9d 100644 --- a/tests/software/bowtie2/align/test.yml +++ b/tests/software/bowtie2/align/test.yml @@ -2,6 +2,7 @@ command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config tags: - bowtie2 + - bowtie2_align - bowtie2_align_single_end files: - path: output/bowtie2/bowtie2/NC_010473.1.bt2 @@ -25,6 +26,7 @@ command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config tags: - bowtie2 + - bowtie2_align - bowtie2_align_paired_end files: - path: output/bowtie2/bowtie2/NC_010473.1.bt2