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https://github.com/MillironX/nf-core_modules.git
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Update samtools modules with config logic (#381)
* fixing paths for test * fixing paths for test * fixing pats to tests * fixing paths to tests * fixing paths to tests * fixing paths for tests * fixing paths for tests * fixing paths for tests * fixing paths fro tests * fixing paths for tests * indentation fixes * typo * renaming test results according to new file name * replacing the md5sums * fixing brackets * replacing md5sums * fixing md5sums * fixing md5sums' * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml Co-authored-by: Ramon Rivera <ramon.rivera10@upr.edu> Co-authored-by: Ramon Rivera <riveravicens@gmail.com>
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arontommi
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15 changed files with 36 additions and 34 deletions
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
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include { SAMTOOLS_FAIDX } from '../../../../software/samtools/faidx/main.nf' addParams( options: [:] )
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workflow test_samtools_faidx {
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fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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SAMTOOLS_FAIDX ( fasta )
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}
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@ -1,8 +1,8 @@
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- name: Run samtools faidx test workflow
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command: nextflow run ./tests/software/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config
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command: nextflow run tests/software/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools_faidx
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files:
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- path: ./output/samtools/test_genome.fasta.fai
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- path: output/samtools/genome.fasta.fai
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md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
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@ -6,7 +6,7 @@ include { SAMTOOLS_FASTQ } from '../../../../software/samtools/fastq/main.nf' ad
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workflow test_samtools_fastq {
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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SAMTOOLS_FASTQ ( input )
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@ -5,6 +5,6 @@
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- samtools_fastq
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files:
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- path: output/samtools/test_2.fastq.gz
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md5sum: 42d3afede8c7ef21577fcd3d07edaa83
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md5sum: 229daf1a62d114cae42c65801e8c0114
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- path: output/samtools/test_1.fastq.gz
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md5sum: 166feed91e5109214b0a7a0d8c53641d
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md5sum: 4cab81f76e66361611621377f1b69d1d
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@ -6,9 +6,9 @@ include { SAMTOOLS_FLAGSTAT } from '../../../../software/samtools/flagstat/main.
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workflow test_samtools_flagstat {
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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]
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SAMTOOLS_FLAGSTAT ( input )
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}
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@ -6,8 +6,9 @@ include { SAMTOOLS_IDXSTATS } from '../../../../software/samtools/idxstats/main.
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workflow test_samtools_idxstats {
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true) ]
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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]
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SAMTOOLS_IDXSTATS ( input )
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}
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@ -6,8 +6,8 @@ include { SAMTOOLS_INDEX } from '../../../../software/samtools/index/main.nf' ad
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workflow test_samtools_index {
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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SAMTOOLS_INDEX ( input )
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}
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@ -1,8 +1,8 @@
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- name: samtools index
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command: nextflow run ./tests/software/samtools/index -entry test_samtools_index -c tests/config/nextflow.config
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command: nextflow run tests/software/samtools/index -entry test_samtools_index -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools_index
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files:
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- path: ./output/samtools/test_paired_end.sorted.bam.bai
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md5sum: d7ef575848d1d13000317e4763b9e502
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- path: output/samtools/test_paired_end.sorted.bam.bai
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md5sum: 704c10dd1326482448ca3073fdebc2f4
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@ -5,11 +5,11 @@ nextflow.enable.dsl = 2
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include { SAMTOOLS_MERGE } from '../../../../software/samtools/merge/main.nf' addParams( options: [:] )
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workflow test_samtools_merge {
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input = [ [ id: 'test' ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam", checkIfExists: true ),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_single_end.sorted.bam", checkIfExists: true) ]
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]
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input = [ [ id: 'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)]
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]
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SAMTOOLS_MERGE ( input )
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}
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@ -6,9 +6,9 @@ include { SAMTOOLS_MPILEUP } from '../../../../software/samtools/mpileup/main.nf
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workflow test_samtools_mpileup {
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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SAMTOOLS_MPILEUP ( input, fasta )
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}
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@ -6,7 +6,7 @@ include { SAMTOOLS_SORT } from '../../../../software/samtools/sort/main.nf' addP
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workflow test_samtools_sort {
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.bam", checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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SAMTOOLS_SORT ( input )
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@ -1,8 +1,8 @@
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- name: samtools sort
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command: nextflow run ./tests/software/samtools/sort -entry test_samtools_sort -c tests/config/nextflow.config
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command: nextflow run tests/software/samtools/sort -entry test_samtools_sort -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools_sort
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files:
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- path: ./output/samtools/test.bam
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md5sum: a10e9a09d887cd3ded9b824a87655b93
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- path: output/samtools/test.bam
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md5sum: 7e32f47768f922a73ccec4dc24db1973
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@ -6,9 +6,9 @@ include { SAMTOOLS_STATS } from '../../../../software/samtools/stats/main.nf' ad
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workflow test_samtools_stats {
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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]
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SAMTOOLS_STATS ( input )
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}
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@ -6,7 +6,8 @@ include { SAMTOOLS_VIEW } from '../../../../software/samtools/view/main.nf' addP
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workflow test_samtools_view {
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.bam", checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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SAMTOOLS_VIEW ( input )
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@ -1,8 +1,8 @@
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- name: samtools view
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command: nextflow run ./tests/software/samtools/view -entry test_samtools_view -c tests/config/nextflow.config
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command: nextflow run tests/software/samtools/view -entry test_samtools_view -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools_view
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files:
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- path: ./output/samtools/test.bam
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md5sum: 7e0d4c8eeff88e8f318eb2fe07dbdc0a
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- path: output/samtools/test.bam
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md5sum: 8fb1e82f76416e9e30fc6b2357e2cf13
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