add docker user option

.gitattributes

@@ -1,2 +1,5 @@
 *.smk linguist-language=Python
 Snakefile linguist-language=Python
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
+

.gitignore

@@ -23,4 +23,6 @@ config/samples.tsv
 workflow/scripts/misc
 .test/workflow/scripts/
 .ipynb_checkpoints
-workflow/scripts/snpEff
+workflow/scripts/snpEff# pixi environments
+.pixi
+

.test/config/config_paired_end.yaml

@@ -1,5 +1,6 @@
 metadata: config/samples.tsv
 pipeline: cpu
+parabricks-docker-user: 1006:1006 # only if using parabricks pipeline at LSTM, otherwise ignore
 
 # Dataset name
 dataset: 'Test-GithubActionsCI'

.test/config/config_single_end.yaml

@@ -1,5 +1,6 @@
 metadata: config/samples.tsv
 pipeline: cpu
+parabricks-docker-user: 1006:1006 # only if using parabricks pipeline at LSTM, otherwise ignore
 
 # Dataset name
 dataset: 'Test-GithubActionsCI'

config/exampleconfig.yaml

@@ -1,6 +1,7 @@
 # RNA-Seq-Pop
-pipeline: parabricks  #parabricks or cpu
 metadata: config/samples.tsv                    # samplesheet metadata file
+pipeline: cpu  # parabricks or cpu
+parabricks-docker-user: 1006:1006 # only if using parabricks pipeline at LSTM, otherwise ignore
 
 dataset: 'Ag_Bouake'                            # Dataset name: Can be anything, will be used to name some main output files
 

workflow/rules/star-haplotypecaller.smk

@@ -44,10 +44,11 @@ rule fq2bam:
     resources:
         all_gpus = 1
     params:
-        wkdir=wkdir
+        wkdir=wkdir,
+        docker_user = config['parabricks-docker-user']
     shell:
         """
-        docker run --user 1006:1006 --rm --gpus all --volume {wkdir}:/workdir --workdir /workdir nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1 \
+        docker run --user {params.docker_user} --rm --gpus all --volume {wkdir}:/workdir --workdir /workdir nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1 \
             pbrun rna_fq2bam \
             --in-fq /workdir/{input.reads[0]} /workdir/{input.reads[1]} \
             --genome-lib-dir /workdir/resources/reference/star_index\
@@ -75,10 +76,11 @@ rule haplotype_caller:
         all_gpus = 1
     params:
         wkdir=wkdir,
+        docker_user = config['parabricks-docker-user'],
         ploidy=config['VariantAnalysis']['ploidy']
     shell:
         """
-        docker run --user 1006:1006 --rm --gpus all --volume {wkdir}:/workdir -w /workdir nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1 \
+        docker run --user {params.docker_user} --rm --gpus all --volume {wkdir}:/workdir -w /workdir nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1 \
             pbrun haplotypecaller \
             --rna \
             --ref /workdir/{input.ref_fasta} \