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Bump version 0.1.5 to chromap/chromap (#1223)

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* Bump version 0.1.5 to chromap/chromap

* Bump conda samtools version to 1.14

* Get read of inconsistent md5sum in conda

* Bump version in conda and retry md5 checks

* genome index md5 hash removed, conda failed
This commit is contained in:
Jose Espinosa-Carrasco 2022-01-20 19:00:20 +01:00 committed by GitHub
parent 435ca4100a
commit 9573e7e53d
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3 changed files with 13 additions and 14 deletions
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16
modules/chromap/chromap/main.nf
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@ -1,13 +1,11 @@
def VERSION = '0.1' // Version information not provided by tool on CLI
process CHROMAP_CHROMAP { process CHROMAP_CHROMAP {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::chromap=0.1 bioconda::samtools=1.13" : null) conda (params.enable_conda ? "bioconda::chromap=0.1.5 bioconda::samtools=1.14" : 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/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' :
'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' }" 'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)
@ -45,7 +43,7 @@ process CHROMAP_CHROMAP {
args_list << "--pairs-natural-chr-order $pairs_chr_order" args_list << "--pairs-natural-chr-order $pairs_chr_order"
} }
def final_args = args_list.join(' ') def final_args = args_list.join(' ')
def compression_cmds = "gzip ${prefix}.${file_extension}" def compression_cmds = "gzip -n ${prefix}.${file_extension}"
if (args.contains("--SAM")) { if (args.contains("--SAM")) {
compression_cmds = """ compression_cmds = """
samtools view $args2 -@ $task.cpus -bh \\ samtools view $args2 -@ $task.cpus -bh \\
@ -67,7 +65,8 @@ process CHROMAP_CHROMAP {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
chromap: $VERSION chromap: \$(echo \$(chromap --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS END_VERSIONS
""" """
} else { } else {
@ -85,7 +84,8 @@ process CHROMAP_CHROMAP {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
chromap: $VERSION chromap: \$(echo \$(chromap --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS END_VERSIONS
""" """
} }

9
tests/modules/chromap/chromap/test.yml
View file

@ -5,9 +5,8 @@
- chromap - chromap
files: files:
- path: output/chromap/genome.index - path: output/chromap/genome.index
md5sum: f889d5f61d80823766af33277d27d386
- path: output/chromap/test.bed.gz - path: output/chromap/test.bed.gz
md5sum: 7029066c27ac6f5ef18d660d5741979a md5sum: 25e40bde24c7b447292cd68573728694
- name: chromap chromap test_chromap_chromap_paired_end - name: chromap chromap test_chromap_chromap_paired_end
command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@ -16,9 +15,8 @@
- chromap - chromap
files: files:
- path: output/chromap/genome.index - path: output/chromap/genome.index
md5sum: f889d5f61d80823766af33277d27d386
- path: output/chromap/test.bed.gz - path: output/chromap/test.bed.gz
md5sum: cafd8fb21977f5ae69e9008b220ab169 md5sum: 7cdc8448882b75811e0c784f5f20aef2
- name: chromap chromap test_chromap_chromap_paired_bam - name: chromap chromap test_chromap_chromap_paired_bam
command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@ -27,6 +25,5 @@
- chromap - chromap
files: files:
- path: output/chromap/genome.index - path: output/chromap/genome.index
md5sum: f889d5f61d80823766af33277d27d386
- path: output/chromap/test.bam - path: output/chromap/test.bam
md5sum: bd1e3fe0f3abd1430ae191754f16a3ed md5sum: 73e2c76007e3c61df625668e01b3f42f

2
tests/modules/chromap/index/test.yml
View file

@ -5,3 +5,5 @@
- chromap - chromap
files: files:
- path: output/chromap/genome.index - path: output/chromap/genome.index