Merge request

.gitlab-ci.yml

-# 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/*

functional_tests/README.md

@@ -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

main.nf

@@ -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}"