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Update version & prefix (#1120)

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* Update version & prefix

* Fix indentation
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FriederikeHanssen 2021-12-07 10:22:32 +01:00 committed by GitHub
parent e22966ce74
commit 7006699ff8
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2 changed files with 58 additions and 45 deletions
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25
modules/seqkit/split2/main.nf
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@ -2,29 +2,30 @@ process SEQKIT_SPLIT2 {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? 'bioconda::seqkit=0.16.1' : null) conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0' : 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' :
'quay.io/biocontainers/seqkit:0.16.1--h9ee0642_0' }" 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)
output: output:
tuple val(meta), path("*${prefix}/*.gz"), emit: reads tuple val(meta), path("**/*.gz"), emit: reads
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
if(meta.single_end){ if(meta.single_end){
""" """
seqkit \\ seqkit \\
split2 \\ split2 \\
$args \\ $args \\
--threads $task.cpus \\ --threads $task.cpus \\
-1 $reads \\ $reads \\
--out-dir $prefix --out-dir ${prefix}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
@ -37,9 +38,9 @@ process SEQKIT_SPLIT2 {
split2 \\ split2 \\
$args \\ $args \\
--threads $task.cpus \\ --threads $task.cpus \\
-1 ${reads[0]} \\ --read1 ${reads[0]} \\
-2 ${reads[1]} \\ --read2 ${reads[1]} \\
--out-dir $prefix --out-dir ${prefix}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

78
tests/modules/seqkit/split2/test.yml
View file

@ -1,83 +1,95 @@
- name: seqkit split2 single-end length - name: seqkit split2 test_seqkit_split2_single_end_length
command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_length -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_length -c tests/config/nextflow.config
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
files: files:
- path: output/seqkit/test/test_1.part_001.fastq.gz - path: output/seqkit/test/test_1.part_001.fastq.gz
md5sum: 6f7d58ba35c254c0817fe9a7c69862e4 md5sum: 7f489b2374c5fcc155a60ce2365a7bb7
- path: output/seqkit/test/test_1.part_002.fastq.gz - path: output/seqkit/test/test_1.part_002.fastq.gz
md5sum: cf38c51506e45380fe25abdd1bd5ccc6 md5sum: 45cccacb4676bca33beb17064322a781
- path: output/seqkit/versions.yml
md5sum: 2d5a709d129be364687cc0b561efa532
- name: seqkit split2 single-end size - name: seqkit split2 test_seqkit_split2_single_end_size
command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_size -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
files: files:
- path: output/seqkit/test/test_1.part_001.fastq.gz - path: output/seqkit/test/test_1.part_001.fastq.gz
md5sum: bf835e685d597fc1ab5e5ac7dd689619 md5sum: b09324606fb3636b51448d6a007d2c71
- path: output/seqkit/test/test_1.part_002.fastq.gz - path: output/seqkit/test/test_1.part_002.fastq.gz
md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54 md5sum: f7873475d463e3b4d21dccbf8e859270
- path: output/seqkit/versions.yml
md5sum: 490d00accd1092a8eca4e83ed809bad3
- name: seqkit split2 single-end part - name: seqkit split2 test_seqkit_split2_single_end_part
command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_part -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
files: files:
- path: output/seqkit/test/test_1.part_001.fastq.gz - path: output/seqkit/test/test_1.part_001.fastq.gz
md5sum: fa25951435471238d5567fd2cae31f55 md5sum: a9d29d08e27246b6d36e21e5def405e3
- path: output/seqkit/test/test_1.part_002.fastq.gz - path: output/seqkit/test/test_1.part_002.fastq.gz
md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a md5sum: 6d547a959adcd027dd1a8734e195dd7d
- path: output/seqkit/test/test_1.part_003.fastq.gz - path: output/seqkit/test/test_1.part_003.fastq.gz
md5sum: 8bc86ba83a611c54f592f4eae19b680f md5sum: 6d63cc8400dd2a96d808514fb18278ee
- path: output/seqkit/versions.yml
md5sum: 90431cd3d28954f656988230d4481115
- name: seqkit split2 paired-end length - name: seqkit split2 test_seqkit_split2_paired_end_length
command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
files: files:
- path: output/seqkit/test/test_1.part_001.fastq.gz - path: output/seqkit/test/test_1.part_001.fastq.gz
md5sum: 6f7d58ba35c254c0817fe9a7c69862e4 md5sum: 7f489b2374c5fcc155a60ce2365a7bb7
- path: output/seqkit/test/test_1.part_002.fastq.gz - path: output/seqkit/test/test_1.part_002.fastq.gz
md5sum: cf38c51506e45380fe25abdd1bd5ccc6 md5sum: 45cccacb4676bca33beb17064322a781
- path: output/seqkit/test/test_2.part_001.fastq.gz - path: output/seqkit/test/test_2.part_001.fastq.gz
md5sum: 6b094b1ba7c439fe44c1bb5e99a02ba4 md5sum: 160b5fd363ff7cad8af9d914269d6426
- path: output/seqkit/test/test_2.part_002.fastq.gz - path: output/seqkit/test/test_2.part_002.fastq.gz
md5sum: 927097c6ac7522199a9e016333181a8e md5sum: 18bc5434cf55706394cccb44e6108561
- path: output/seqkit/versions.yml
md5sum: 9272afc1a126ae997a712edeef317f22
- name: seqkit split2 paired-end size - name: seqkit split2 test_seqkit_split2_paired_end_size
command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
files: files:
- path: output/seqkit/test/test_1.part_001.fastq.gz - path: output/seqkit/test/test_1.part_001.fastq.gz
md5sum: bf835e685d597fc1ab5e5ac7dd689619 md5sum: b09324606fb3636b51448d6a007d2c71
- path: output/seqkit/test/test_1.part_002.fastq.gz - path: output/seqkit/test/test_1.part_002.fastq.gz
md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54 md5sum: f7873475d463e3b4d21dccbf8e859270
- path: output/seqkit/test/test_2.part_001.fastq.gz - path: output/seqkit/test/test_2.part_001.fastq.gz
md5sum: 09d0dd83b5b1b9b95d316eeed79ea5ba md5sum: c0602b62aae860dd284c0eb0062c24dd
- path: output/seqkit/test/test_2.part_002.fastq.gz - path: output/seqkit/test/test_2.part_002.fastq.gz
md5sum: 8796c3f327b1094244bfcdb36d536526 md5sum: 5bc7a98b618100b29910eb41c4c9ac0d
- path: output/seqkit/versions.yml
md5sum: af66912ae8abc493f77f70e3bf473144
- name: seqkit split2 paired-end part - name: seqkit split2 test_seqkit_split2_paired_end_part
command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config
tags: tags:
- seqkit - seqkit
- seqkit/split2 - seqkit/split2
files: files:
- path: output/seqkit/test/test_1.part_001.fastq.gz - path: output/seqkit/test/test_1.part_001.fastq.gz
md5sum: fa25951435471238d5567fd2cae31f55 md5sum: a9d29d08e27246b6d36e21e5def405e3
- path: output/seqkit/test/test_1.part_002.fastq.gz - path: output/seqkit/test/test_1.part_002.fastq.gz
md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a md5sum: 6d547a959adcd027dd1a8734e195dd7d
- path: output/seqkit/test/test_1.part_003.fastq.gz - path: output/seqkit/test/test_1.part_003.fastq.gz
md5sum: 8bc86ba83a611c54f592f4eae19b680f md5sum: 6d63cc8400dd2a96d808514fb18278ee
- path: output/seqkit/test/test_2.part_001.fastq.gz - path: output/seqkit/test/test_2.part_001.fastq.gz
md5sum: f0055c99cd193fd97466b3cde9dd1b8f md5sum: b51a1bed106e4ec0c9be7d9e224d0616
- path: output/seqkit/test/test_2.part_002.fastq.gz - path: output/seqkit/test/test_2.part_002.fastq.gz
md5sum: 8a90df768201785f7a7cd5dbb41e846a md5sum: 079078a7f86114ae29cda8c00d5a7fc9
- path: output/seqkit/test/test_2.part_003.fastq.gz - path: output/seqkit/test/test_2.part_003.fastq.gz
md5sum: 890b90083e8e1606bd13ba34149cedd7 md5sum: 6987941bf8c4a37565e333029ba41ca0
- path: output/seqkit/versions.yml
md5sum: 193bc5f0c429076f816ab0a529c4c1fc