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Bump chromap version 0.2.0 (#1374)

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* Bump chromap version 0.2.0

* Temporary use the docker container until singularity container becomes available

* Temporary use the docker container until singularity container available

* Remove empty lines

* Update singularity container after became available
This commit is contained in:
Jose Espinosa-Carrasco 2022-03-10 09:23:45 +01:00 committed by GitHub
parent 24f0bdd14e
commit 62da45b0e1
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GPG key ID: 4AEE18F83AFDEB23
4 changed files with 15 additions and 8 deletions
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6
modules/chromap/chromap/main.nf
View file

@ -2,10 +2,10 @@ process CHROMAP_CHROMAP {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::chromap=0.1.5 bioconda::samtools=1.14" : null) conda (params.enable_conda ? "bioconda::chromap=0.2.0 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-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' :
'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' }" 'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)

7
modules/chromap/index/main.nf
View file

@ -2,11 +2,10 @@ process CHROMAP_INDEX {
tag '$fasta' tag '$fasta'
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::chromap=0.1.5" : null) conda (params.enable_conda ? "bioconda::chromap=0.2.0" : 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/chromap:0.1.5--h9a82719_0' : 'https://depot.galaxyproject.org/singularity/chromap:0.2.0--hd03093a_1' :
'quay.io/biocontainers/chromap:0.1.5--h9a82719_0' }" 'quay.io/biocontainers/chromap:0.2.0--hd03093a_1' }"
input: input:
path fasta path fasta

8
tests/modules/chromap/chromap/test.yml
View file

@ -7,6 +7,8 @@
- path: output/chromap/genome.index - path: output/chromap/genome.index
- path: output/chromap/test.bed.gz - path: output/chromap/test.bed.gz
md5sum: 25e40bde24c7b447292cd68573728694 md5sum: 25e40bde24c7b447292cd68573728694
- path: output/chromap/versions.yml
md5sum: 2d3d2959ac20d98036807964896829e7
- 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
@ -17,6 +19,8 @@
- path: output/chromap/genome.index - path: output/chromap/genome.index
- path: output/chromap/test.bed.gz - path: output/chromap/test.bed.gz
md5sum: 7cdc8448882b75811e0c784f5f20aef2 md5sum: 7cdc8448882b75811e0c784f5f20aef2
- path: output/chromap/versions.yml
md5sum: 51cff66779161d8a602cce5989017395
- 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
@ -26,4 +30,6 @@
files: files:
- path: output/chromap/genome.index - path: output/chromap/genome.index
- path: output/chromap/test.bam - path: output/chromap/test.bam
md5sum: 73e2c76007e3c61df625668e01b3f42f md5sum: f255c7441d5a1f307fc642d2aa19647e
- path: output/chromap/versions.yml
md5sum: f91910c44169549c3923931de5c3afcb

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
- path: output/chromap/versions.yml
md5sum: b75dec647f9dc5f4887f36d1db7a9ccd