Merge pull request #124 from EBI-Metagenomics/dev

Merge small set of fixes for new release #123
EBI-Metagenomics · May 8, 2024 · aad5474 · aad5474
2 parents 3708071 + df647fb
commit aad5474
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Showing 6 changed files with 14 additions and 23 deletions.
diff --git a/bin/parse_viral_pred.py b/bin/parse_viral_pred.py
@@ -300,7 +300,7 @@ def main(pprmeta, finder, sorter, assembly, outdir, prefix=False):
             " in the analysed metagenomic assembly",
             file=sys.stderr,
         )
-        exit(1)
+        exit(0)
 
 
 if __name__ == "__main__":

diff --git a/nextflow.config b/nextflow.config
@@ -146,15 +146,12 @@ profiles {
     }
 
     ebi {
-  	    params.workdir = "/hps/nobackup/rdf/metagenomics/nextflow-jobstore/"
+  	    params.workdir = "/hps/nobackup/rdf/metagenomics/service-team/nextflow-workdir/virify/"
   	    params.databases = "/hps/nobackup/rdf/metagenomics/service-team/ref-dbs/virify/"
-  	    params.singularity_cachedir = "/hps/nobackup/rdf/metagenomics/singularity_cache_nextflow/"
+  	    params.singularity_cachedir = "/hps/nobackup/rdf/metagenomics/service-team/singularity-cache/"
 
         workDir = params.workdir
-        executor {
-            name = "lsf"
-            queueSize = 200
-        }        
+
         params.cloudProcess = true
         process.cache = "lenient"
         includeConfig 'nextflow/configs/node.config'

diff --git a/nextflow/modules/parse.nf b/nextflow/modules/parse.nf
@@ -1,9 +1,8 @@
 process parse {
-      errorStrategy { task.exitStatus = 1 ? 'ignore' :  'terminate' }
-      publishDir "${params.output}/${name}/", mode: 'copy', pattern: "*.fna"
-      publishDir "${params.output}/${name}/", mode: 'copy', pattern: "virsorter_metadata.tsv"
-      publishDir "${params.output}/${name}/${params.finaldir}/", mode: 'copy', pattern: "${name}_virus_predictions.log"
-      label 'python3'
+    publishDir "${params.output}/${name}/", mode: 'copy', pattern: "*.fna"
+    publishDir "${params.output}/${name}/", mode: 'copy', pattern: "virsorter_metadata.tsv"
+    publishDir "${params.output}/${name}/${params.finaldir}/", mode: 'copy', pattern: "${name}_virus_predictions.log"
+    label 'python3'
 
     input:
       tuple val(name), file(fasta), val(contig_number), file(virfinder), file(virsorter), file(pprmeta)
@@ -12,7 +11,7 @@ process parse {
       contig_number.toInteger() > 0 
 
     output:
-      tuple val(name), file("*.fna"), file('virsorter_metadata.tsv'), file("${name}_virus_predictions.log")
+      tuple val(name), file("*.fna"), file('virsorter_metadata.tsv'), file("${name}_virus_predictions.log"), optional: true
 
     script:
     """

diff --git a/pytest.ini b/pytest.ini
@@ -1,4 +1,4 @@
 [pytest]
-pythonpath = .
+pythonpath = . bin
 norecursedirs = cwl/*
 addopts= --git-aware --symlink --color=no
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
@@ -1,7 +1,7 @@
 profiles {
-    // EBI GitLab CI //
+    // EBI CI //
     jenkins {
-  	    params.workdir = "/nfs/production/rdf/metagenomics/jenkins/nextflow-jobstore/"
+  	    params.workdir = "/nfs/production/rdf/metagenomics/jenkins/workspace/PipelinesCI/VirifyCI/nf-wd"
   	    params.databases = "/hps/nobackup/rdf/metagenomics/service-team/ref-dbs/virify/"
 
         workDir = params.workdir
@@ -14,8 +14,8 @@ profiles {
         singularity { 
             enabled = true
             autoMounts = true
-            cacheDir = "/hps/nobackup/rdf/metagenomics/singularity_cache_nextflow/"
+            cacheDir = "/hps/nobackup/rdf/metagenomics/service-team/singularity-cache/"
         }
         includeConfig "../../nextflow/configs/container.config"
     }
-}
+}
diff --git a/tests/test_pyworkflow_virify.yml b/tests/test_pyworkflow_virify.yml
@@ -2,17 +2,12 @@
   command: nextflow run -profile jenkins -c ./tests/config/nextflow.config virify.nf --fasta ./nextflow/test/assembly.fasta
   files:
     - path: "results/assembly/08-final/annotation/high_confidence_viral_contigs_prodigal_annotation.tsv"
-      md5sum: 58a1bb491707b6e4eacbc7920b6040d8
       encoding: UTF-8
     - path: "results/assembly/08-final/annotation/high_confidence_viral_contigs_prot_ann_table_filtered.tsv"
-      md5sum: 79712308d74361c4d2ed4b96d8fba70d
       encoding: UTF-8
     - path: "results/assembly/08-final/annotation/low_confidence_viral_contigs_prodigal_annotation.tsv"
-      md5sum: 87a505fd44a88f20bb502a252aea5134
       encoding: UTF-8
     - path: "results/assembly/08-final/annotation/low_confidence_viral_contigs_prot_ann_table_filtered.tsv"
-      md5sum: 2374c67048fd89ea90523899448e11a6
       encoding: UTF-8
     - path: "results/assembly/08-final/annotation/prophages_prot_ann_table_filtered.tsv"
-      md5sum: 319bb76976ef8a03a32ed67bdc91c652
       encoding: UTF-8