Commit 82951f63 authored by MARTIN Pierre's avatar MARTIN Pierre
Browse files

Merge branch 'dev' into 'dsl2'

# Conflicts:
#   README.md
#   bin/aln2taxaffi.py
#   conf/base.config
#   conf/test_genotoul_workq.config
#   docs/README.md
#   docs/installation.md
#   docs/usage.md
#   functional_tests/main.py
#   main.nf
#   nextflow.config
parents c47901c1 02a9545e
Pipeline #46463 skipped with stages
......@@ -29,7 +29,7 @@ singularity-image:
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 "${CI_REGISTRY_PASSWORD}" metagWGS.sif oras://"$CI_REGISTRY_IMAGE"/metagWGS:"$CI_COMMIT_TAG"
- singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" eggnog_mapper.sif oras://"$CI_REGISTRY_IMAGE"/eggnog_mapper:"$CI_COMMIT_TAG"
- singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" mosdepth.sif oras://"$CI_REGISTRY_IMAGE"/mosdepth:"$CI_COMMIT_TAG"
only:
......
......@@ -50,7 +50,7 @@ process {
}
withName: QUAST {
cpus = 4
memory = { 8.GB * task.attempt }
memory = { 32.GB * task.attempt }
}
withName: READS_DEDUPLICATION {
memory = { 32.GB * task.attempt }
......
process.beforeScript = 'echo $HOSTNAME'
trace {
enabled = true
file = 'pipeline_trace.txt'
fields = 'task_id,name,status,exit,realtime,%cpu,rss,script'
}
\ No newline at end of file
......@@ -81,6 +81,20 @@ process {
```
Where \<PATH\> leads to the directory where the singularity images are built/downloaded.
**WARNING:** to ensure Nextflow can find the _.sif_ files, we encourage you to change the _nextflow.config_ file in metagWGS at these lines:
```
process {
container = '<PATH>/metagwgs.sif'
withLabel: eggnog {
container = '<PATH>/eggnog_mapper.sif'
}
withLabel: mosdepth {
container = '<PATH>/mosdepth.sif'
}
}
```
Where \<PATH\> leads to the directory where the singularity images are built/downloaded.
## V. Use metagWGS
See the [Usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/docs/usage.md) documentation to know how to run metagWGS.
......@@ -59,6 +59,7 @@ dependencies:
- future=0.18.2
- gcc_impl_linux-64=7.5.0
- gcc_linux-64=7.5.0
- genometools-genometools=1.6.1
- gettext=0.19.8.1
- gfortran_impl_linux-64=7.5.0
- gfortran_linux-64=7.5.0
......
......@@ -38,6 +38,7 @@ include { MULTIQC } from './modules/multiqc'
--host_bwa_index Full path to directory containing BWA index including base name i.e ("PATH/name_genome.{amb,ann,bwt,pac,sa}").
You need to use --skip_host_filter or --host_fasta or --skip_01_clean_qc. If it is not the case, an error message will occur.
--skip_kaiju Skip taxonomic affiliation of reads with kaiju.
--kaiju_verbose Allow the generation of kaiju verbose output (file can be large)
--kaiju_db_dir Directory with kaiju database already built ("PATH/directory").
--kaiju_db_url Indicate kaiju database you want to build. Default: "https://kaiju.binf.ku.dk/database/kaiju_db_refseq_2021-02-26.tgz".
You need to use --kaiju_db_url or --kaiju_db_dir or --skip_kaiju. If it is not the case, an error message will occur.
......
......@@ -70,6 +70,17 @@ params {
// Load base.config by default for all pipelines.
includeConfig 'conf/base.config'
// Location of each singularity image (modify with proper path)
process {
container = '/home/pmartin2/work/metaG/singularity_img/metagwgs.sif'
withLabel: eggnog {
container = '/home/pmartin2/work/metaG/singularity_img/eggnog_mapper.sif'
}
withLabel: mosdepth {
container = '/home/pmartin2/work/metaG/singularity_img/mosdepth.sif'
}
}
// Define profiles.
profiles {
debug { includeConfig 'conf/debug.config' }
......
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