Commit 853f098b authored by MARTIN Pierre's avatar MARTIN Pierre
Browse files

Merge request

parent 39f4c22c
# recipe for building singularity image and deploy it on the registery for bwa version 0.7.17
image:
name: quay.io/singularity/singularity:v3.4.0
entrypoint: [""]
stages:
- build
- deploy
# Build Singularity container bwa_v0.7.17.sif
singularity-image:
stage: build
script:
- singularity build metagWGS.sif env/Singularity_recipe_metagWGS
- singularity build eggnog_mapper.sif env/Singularity_recipe_eggnog_mapper
artifacts:
paths:
- metagWGS.sif
- eggnog_mapper.sif
only:
changes:
- .gitlab-ci.yml
- env/*
# Push the image template.sif on the registry
deploy:
stage: deploy
script:
- singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" metagWGS.sif oras://"$CI_REGISTRY_IMAGE"/"$CI_PROJECT_NAME":"$CI_COMMIT_TAG"
- singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" eggnog_mapper.sif oras://"$CI_REGISTRY_IMAGE"/eggnog_mapper:"$CI_COMMIT_TAG"
only:
changes:
- .gitlab-ci.yml
- env/*
......@@ -121,4 +121,4 @@ Not tested: 0
If a test resulted in 'Failed' instead of 'Passed', the stdout is printed in log.
Sometimes, files are not tested because present in exp_dir but not in obs_dir. Then a log ft_\[step\].not_tested if created containing names of missing files. In 02_assembly, there are two possible assembly programs that can be used: metaspades and megahit, resulting in this .not_tested log file. Not tested files are not counted in missed count.
\ No newline at end of file
Sometimes, files are not tested because present in exp_dir but not in obs_dir. Then a log ft_\[step\].not_tested is created containing names of missing files. In 02_assembly, there are two possible assembly programs that can be used: metaspades and megahit, resulting in this .not_tested log file. Not tested files are not counted in missed count.
\ No newline at end of file
......@@ -544,7 +544,7 @@ process assembly {
output:
set sampleId, file("${params.assembly}/${sampleId}.contigs.fa") into assembly_for_quast_ch, assembly_for_dedup_ch, assembly_for_filter_ch, assembly_no_filter_ch
set sampleId, file("${params.assembly}/${sampleId}.log"), file("${params.assembly}/params.txt") into logs_assembly_ch
set sampleId, file("${params.assembly}/${sampleId}.log"), file("${params.assembly}/${sampleId}.params.txt") into logs_assembly_ch
when: ('02_assembly' in step || '03_filtering' in step || '04_structural_annot' in step || '05_alignment' in step || '06_func_annot' in step || '07_taxo_affi' in step || '08_binning' in step)
......@@ -558,6 +558,7 @@ process assembly {
else if(params.assembly=='megahit')
"""
megahit -t ${task.cpus} -1 ${preprocessed_reads_R1} -2 ${preprocessed_reads_R2} -o ${params.assembly} --out-prefix "${sampleId}"
mv options.json params.txt
"""
else
error "Invalid parameter: ${params.assembly}"
......
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