Merge pull request #28 from nf-core/fix_conda_env_for_local_module

Use jq sequera containers

modules/local/multiqc_assemblyscan_plot_data_environment.yml → modules/local/multiqc_assemblyscan_plot_data/environment.yml

@@ -1,6 +1,5 @@
 channels:
   - conda-forge
   - bioconda
-
 dependencies:
-  - bioconda::jq=1.6
+  - conda-forge::jq=1.7.1

modules/local/multiqc_assemblyscan_plot_data.nf → modules/local/multiqc_assemblyscan_plot_data/main.nf

@@ -1,9 +1,11 @@
 process MULTIQC_ASSEMBLYSCAN_PLOT_DATA {
+    tag "${json.baseName}"
     label 'process_single'
-    conda "${moduleDir}/multiqc_assemblyscan_plot_data_environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/jq:1.6':
-        'biocontainers/jq:1.6' }"
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/84/84eef7b4cd5f6304aa5ba9ac6b0051850af300abefb615b72b776d1245990749/data'
+        : 'community.wave.seqera.io/library/jq:fee8aafd41d9e3aa' }"
 
     // This module parses the JSON output of the assemblyscan module with jq to extract
     // statistics about GC content and contig length.  I do not know how to contribute
@@ -13,13 +15,12 @@ process MULTIQC_ASSEMBLYSCAN_PLOT_DATA {
     path(json)
 
     output:
-    path "*_mqc.tsv",  emit: tsv
+    path ("*_mqc.tsv"),  emit: tsv
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
     """
     echo "# id: 'base_content_summary'" > gc_summary_mqc.tsv
     echo "# section_name: 'Base frequency'" >> gc_summary_mqc.tsv
@@ -31,7 +32,7 @@ process MULTIQC_ASSEMBLYSCAN_PLOT_DATA {
     echo "#    title: 'per_base content and percentage'" >> gc_summary_mqc.tsv
     echo "#    ylab: ''" >> gc_summary_mqc.tsv
     echo "id\tpercent_A\tpercent_C\tpercent_G\tpercent_T\tpercent_N\tcontig_non_ACGTN" >> gc_summary_mqc.tsv
-    for i in $json
+    for i in ${json}
     do
         printf "\$(basename \$i .json)\t" >> gc_summary_mqc.tsv
         jq -r '[.contig_percent_a, .contig_percent_c, .contig_percent_g, .contig_percent_t, .contig_percent_n, .contig_non_acgtn] | @tsv' \$i >> gc_summary_mqc.tsv
@@ -47,7 +48,7 @@ process MULTIQC_ASSEMBLYSCAN_PLOT_DATA {
     echo "#    title: 'contigs length statistics'" >> contig_length_mqc.tsv
     echo "#    ylab: 'length'" >> contig_length_mqc.tsv
     echo "id\tTOTALcontiglen\tMINcontiglen\tMAXcontiglen\ttotalcontigs\tcontigs>1k\tcontigs>10k" >> contig_length_mqc.tsv
-    for i in $json
+    for i in ${json}
     do
         printf "\$(basename \$i .json)\t" >> contig_length_mqc.tsv
         jq -r '[.total_contig_length, .min_contig_length, .max_contig_length, .total_contig, .contigs_greater_1k, .contigs_greater_10k] | @tsv' \$i >> contig_length_mqc.tsv

workflows/pairgenomealign.nf

@@ -5,7 +5,7 @@
 */
 
 include { ASSEMBLYSCAN                     } from '../modules/nf-core/assemblyscan/main'
-include { MULTIQC_ASSEMBLYSCAN_PLOT_DATA   } from '../modules/local/multiqc_assemblyscan_plot_data'
+include { MULTIQC_ASSEMBLYSCAN_PLOT_DATA   } from '../modules/local/multiqc_assemblyscan_plot_data/main'
 include { PAIRALIGN_M2M                    } from '../subworkflows/local/pairalign_m2m/main'
 include { SEQTK_CUTN as CUTN_TARGET        } from '../modules/nf-core/seqtk/cutn/main'
 include { SEQTK_CUTN as CUTN_QUERY         } from '../modules/nf-core/seqtk/cutn/main'