From 743ba37d4ba3c6dd2b5edea3f238f167a2190d08 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 3 Feb 2021 16:04:43 +0000 Subject: [PATCH] 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