mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
Update version & prefix (#1120)
* Update version & prefix * Fix indentation
This commit is contained in:
FriederikeHanssen
GitHub
parent
e22966ce74
commit
7006699ff8
2 changed files with 58 additions and 45 deletions
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@ -2,29 +2,30 @@ process SEQKIT_SPLIT2 {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::seqkit=0.16.1' : null)
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conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0' :
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'quay.io/biocontainers/seqkit:0.16.1--h9ee0642_0' }"
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'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' :
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'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*${prefix}/*.gz"), emit: reads
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tuple val(meta), path("**/*.gz"), emit: reads
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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def prefix = task.ext.prefix ?: "${meta.id}"
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if(meta.single_end){
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"""
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seqkit \\
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split2 \\
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$args \\
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--threads $task.cpus \\
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-1 $reads \\
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--out-dir $prefix
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$reads \\
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--out-dir ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -37,9 +38,9 @@ process SEQKIT_SPLIT2 {
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split2 \\
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$args \\
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--threads $task.cpus \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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--out-dir $prefix
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--read1 ${reads[0]} \\
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--read2 ${reads[1]} \\
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--out-dir ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -1,83 +1,95 @@
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- name: seqkit split2 single-end length
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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
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- name: seqkit split2 test_seqkit_split2_single_end_length
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command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_length -c tests/config/nextflow.config
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tags:
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- seqkit
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- seqkit/split2
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files:
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- path: output/seqkit/test/test_1.part_001.fastq.gz
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md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
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md5sum: 7f489b2374c5fcc155a60ce2365a7bb7
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- path: output/seqkit/test/test_1.part_002.fastq.gz
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md5sum: cf38c51506e45380fe25abdd1bd5ccc6
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md5sum: 45cccacb4676bca33beb17064322a781
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- path: output/seqkit/versions.yml
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md5sum: 2d5a709d129be364687cc0b561efa532
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- name: seqkit split2 single-end size
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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
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- name: seqkit split2 test_seqkit_split2_single_end_size
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command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
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tags:
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- seqkit
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- seqkit/split2
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files:
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- path: output/seqkit/test/test_1.part_001.fastq.gz
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md5sum: bf835e685d597fc1ab5e5ac7dd689619
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md5sum: b09324606fb3636b51448d6a007d2c71
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- path: output/seqkit/test/test_1.part_002.fastq.gz
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md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54
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md5sum: f7873475d463e3b4d21dccbf8e859270
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- path: output/seqkit/versions.yml
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md5sum: 490d00accd1092a8eca4e83ed809bad3
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- name: seqkit split2 single-end part
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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
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- name: seqkit split2 test_seqkit_split2_single_end_part
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command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config
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tags:
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- seqkit
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- seqkit/split2
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files:
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- path: output/seqkit/test/test_1.part_001.fastq.gz
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md5sum: fa25951435471238d5567fd2cae31f55
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md5sum: a9d29d08e27246b6d36e21e5def405e3
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- path: output/seqkit/test/test_1.part_002.fastq.gz
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md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a
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md5sum: 6d547a959adcd027dd1a8734e195dd7d
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- path: output/seqkit/test/test_1.part_003.fastq.gz
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md5sum: 8bc86ba83a611c54f592f4eae19b680f
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md5sum: 6d63cc8400dd2a96d808514fb18278ee
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- path: output/seqkit/versions.yml
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md5sum: 90431cd3d28954f656988230d4481115
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- name: seqkit split2 paired-end length
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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
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- name: seqkit split2 test_seqkit_split2_paired_end_length
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command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config
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tags:
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- seqkit
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- seqkit/split2
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files:
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- path: output/seqkit/test/test_1.part_001.fastq.gz
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md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
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md5sum: 7f489b2374c5fcc155a60ce2365a7bb7
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- path: output/seqkit/test/test_1.part_002.fastq.gz
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md5sum: cf38c51506e45380fe25abdd1bd5ccc6
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md5sum: 45cccacb4676bca33beb17064322a781
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- path: output/seqkit/test/test_2.part_001.fastq.gz
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md5sum: 6b094b1ba7c439fe44c1bb5e99a02ba4
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md5sum: 160b5fd363ff7cad8af9d914269d6426
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- path: output/seqkit/test/test_2.part_002.fastq.gz
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md5sum: 927097c6ac7522199a9e016333181a8e
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md5sum: 18bc5434cf55706394cccb44e6108561
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- path: output/seqkit/versions.yml
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md5sum: 9272afc1a126ae997a712edeef317f22
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- name: seqkit split2 paired-end size
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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
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- name: seqkit split2 test_seqkit_split2_paired_end_size
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command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config
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tags:
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- seqkit
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- seqkit/split2
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files:
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- path: output/seqkit/test/test_1.part_001.fastq.gz
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md5sum: bf835e685d597fc1ab5e5ac7dd689619
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md5sum: b09324606fb3636b51448d6a007d2c71
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- path: output/seqkit/test/test_1.part_002.fastq.gz
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md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54
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md5sum: f7873475d463e3b4d21dccbf8e859270
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- path: output/seqkit/test/test_2.part_001.fastq.gz
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md5sum: 09d0dd83b5b1b9b95d316eeed79ea5ba
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md5sum: c0602b62aae860dd284c0eb0062c24dd
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- path: output/seqkit/test/test_2.part_002.fastq.gz
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md5sum: 8796c3f327b1094244bfcdb36d536526
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md5sum: 5bc7a98b618100b29910eb41c4c9ac0d
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- path: output/seqkit/versions.yml
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md5sum: af66912ae8abc493f77f70e3bf473144
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- name: seqkit split2 paired-end part
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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
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- name: seqkit split2 test_seqkit_split2_paired_end_part
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command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config
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tags:
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- seqkit
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- seqkit/split2
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files:
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- path: output/seqkit/test/test_1.part_001.fastq.gz
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md5sum: fa25951435471238d5567fd2cae31f55
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md5sum: a9d29d08e27246b6d36e21e5def405e3
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- path: output/seqkit/test/test_1.part_002.fastq.gz
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md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a
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md5sum: 6d547a959adcd027dd1a8734e195dd7d
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- path: output/seqkit/test/test_1.part_003.fastq.gz
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md5sum: 8bc86ba83a611c54f592f4eae19b680f
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md5sum: 6d63cc8400dd2a96d808514fb18278ee
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- path: output/seqkit/test/test_2.part_001.fastq.gz
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md5sum: f0055c99cd193fd97466b3cde9dd1b8f
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md5sum: b51a1bed106e4ec0c9be7d9e224d0616
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- path: output/seqkit/test/test_2.part_002.fastq.gz
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md5sum: 8a90df768201785f7a7cd5dbb41e846a
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md5sum: 079078a7f86114ae29cda8c00d5a7fc9
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- path: output/seqkit/test/test_2.part_003.fastq.gz
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md5sum: 890b90083e8e1606bd13ba34149cedd7
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md5sum: 6987941bf8c4a37565e333029ba41ca0
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- path: output/seqkit/versions.yml
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md5sum: 193bc5f0c429076f816ab0a529c4c1fc
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