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Update samtools modules with config logic (#381)

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* 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>
This commit is contained in:
arontommi 2021-03-24 19:15:30 +01:00 committed by GitHub
parent 889465cb2b
commit d162f21ab3
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GPG key ID: 4AEE18F83AFDEB23
15 changed files with 36 additions and 34 deletions
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2
tests/software/samtools/faidx/main.nf
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { SAMTOOLS_FAIDX } from '../../../../software/samtools/faidx/main.nf' addParams( options: [:] ) include { SAMTOOLS_FAIDX } from '../../../../software/samtools/faidx/main.nf' addParams( options: [:] )
workflow test_samtools_faidx { workflow test_samtools_faidx {
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
SAMTOOLS_FAIDX ( fasta ) SAMTOOLS_FAIDX ( fasta )
} }

4
tests/software/samtools/faidx/test.yml
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@ -1,8 +1,8 @@
- name: Run samtools faidx test workflow - name: Run samtools faidx test workflow
command: nextflow run ./tests/software/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config command: nextflow run tests/software/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config
tags: tags:
- samtools - samtools
- samtools_faidx - samtools_faidx
files: files:
- path: ./output/samtools/test_genome.fasta.fai - path: output/samtools/genome.fasta.fai
md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5 md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5

2
tests/software/samtools/fastq/main.nf
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@ -6,7 +6,7 @@ include { SAMTOOLS_FASTQ } from '../../../../software/samtools/fastq/main.nf' ad
workflow test_samtools_fastq { workflow test_samtools_fastq {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
] ]
SAMTOOLS_FASTQ ( input ) SAMTOOLS_FASTQ ( input )

4
tests/software/samtools/fastq/test.yml
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@ -5,6 +5,6 @@
- samtools_fastq - samtools_fastq
files: files:
- path: output/samtools/test_2.fastq.gz - path: output/samtools/test_2.fastq.gz
md5sum: 42d3afede8c7ef21577fcd3d07edaa83 md5sum: 229daf1a62d114cae42c65801e8c0114
- path: output/samtools/test_1.fastq.gz - path: output/samtools/test_1.fastq.gz
md5sum: 166feed91e5109214b0a7a0d8c53641d md5sum: 4cab81f76e66361611621377f1b69d1d

4
tests/software/samtools/flagstat/main.nf
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@ -6,8 +6,8 @@ include { SAMTOOLS_FLAGSTAT } from '../../../../software/samtools/flagstat/main.
workflow test_samtools_flagstat { workflow test_samtools_flagstat {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
SAMTOOLS_FLAGSTAT ( input ) SAMTOOLS_FLAGSTAT ( input )

5
tests/software/samtools/idxstats/main.nf
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@ -6,8 +6,9 @@ include { SAMTOOLS_IDXSTATS } from '../../../../software/samtools/idxstats/main.
workflow test_samtools_idxstats { workflow test_samtools_idxstats {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]
SAMTOOLS_IDXSTATS ( input ) SAMTOOLS_IDXSTATS ( input )
} }

2
tests/software/samtools/index/main.nf
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@ -6,7 +6,7 @@ include { SAMTOOLS_INDEX } from '../../../../software/samtools/index/main.nf' ad
workflow test_samtools_index { workflow test_samtools_index {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
] ]
SAMTOOLS_INDEX ( input ) SAMTOOLS_INDEX ( input )

6
tests/software/samtools/index/test.yml
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@ -1,8 +1,8 @@
- name: samtools index - name: samtools index
command: nextflow run ./tests/software/samtools/index -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: tags:
- samtools - samtools
- samtools_index - samtools_index
files: files:
- path: ./output/samtools/test_paired_end.sorted.bam.bai - path: output/samtools/test_paired_end.sorted.bam.bai
md5sum: d7ef575848d1d13000317e4763b9e502 md5sum: 704c10dd1326482448ca3073fdebc2f4

6
tests/software/samtools/merge/main.nf
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@ -6,9 +6,9 @@ include { SAMTOOLS_MERGE } from '../../../../software/samtools/merge/main.nf' ad
workflow test_samtools_merge { workflow test_samtools_merge {
input = [ [ id: 'test' ], // meta map input = [ [ id: 'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam", checkIfExists: true ), [ file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_single_end.sorted.bam", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)]
] ]
SAMTOOLS_MERGE ( input ) SAMTOOLS_MERGE ( input )

2
tests/software/samtools/mpileup/main.nf
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@ -6,7 +6,7 @@ include { SAMTOOLS_MPILEUP } from '../../../../software/samtools/mpileup/main.nf
workflow test_samtools_mpileup { workflow test_samtools_mpileup {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)

2
tests/software/samtools/sort/main.nf
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@ -6,7 +6,7 @@ include { SAMTOOLS_SORT } from '../../../../software/samtools/sort/main.nf' addP
workflow test_samtools_sort { workflow test_samtools_sort {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
] ]
SAMTOOLS_SORT ( input ) SAMTOOLS_SORT ( input )

6
tests/software/samtools/sort/test.yml
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@ -1,8 +1,8 @@
- name: samtools sort - name: samtools sort
command: nextflow run ./tests/software/samtools/sort -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: tags:
- samtools - samtools
- samtools_sort - samtools_sort
files: files:
- path: ./output/samtools/test.bam - path: output/samtools/test.bam
md5sum: a10e9a09d887cd3ded9b824a87655b93 md5sum: 7e32f47768f922a73ccec4dc24db1973

4
tests/software/samtools/stats/main.nf
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@ -6,8 +6,8 @@ include { SAMTOOLS_STATS } from '../../../../software/samtools/stats/main.nf' ad
workflow test_samtools_stats { workflow test_samtools_stats {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
SAMTOOLS_STATS ( input ) SAMTOOLS_STATS ( input )

3
tests/software/samtools/view/main.nf
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@ -6,7 +6,8 @@ include { SAMTOOLS_VIEW } from '../../../../software/samtools/view/main.nf' addP
workflow test_samtools_view { workflow test_samtools_view {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
] ]
SAMTOOLS_VIEW ( input ) SAMTOOLS_VIEW ( input )

6
tests/software/samtools/view/test.yml
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@ -1,8 +1,8 @@
- name: samtools view - name: samtools view
command: nextflow run ./tests/software/samtools/view -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: tags:
- samtools - samtools
- samtools_view - samtools_view
files: files:
- path: ./output/samtools/test.bam - path: output/samtools/test.bam
md5sum: 7e0d4c8eeff88e8f318eb2fe07dbdc0a md5sum: 8fb1e82f76416e9e30fc6b2357e2cf13