Merge pull request #26 from ctg-lund/dev

Hotfixes
ctg-lund · Jun 26, 2023 · badb484 · badb484
2 parents 8ae9c7b + 458a803
commit badb484
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/modules/cellranger2multiqc/multi/main.nf b/modules/cellranger2multiqc/multi/main.nf
@@ -28,7 +28,7 @@ process CELLRANGER_MULTI_TO_MULTIQC{
     # Convert the cellranger multi csv output to json
     for file in $params.outdir/$project_id/2_multi/*/outs/per_sample_outs/*
     do
-        python multimetric2mqc.py $file/metrics_summary.csv \$(basename \$file)
+        python multimetric2mqc.py \$file/metrics_summary.csv \$(basename \$file)
     done
     
     # Populate the multiqc config files

diff --git a/modules/multi_config/generate_lib/main.nf b/modules/multi_config/generate_lib/main.nf
@@ -38,6 +38,6 @@ process GENERATE_LIB_CSV{
     """
     echo \"\"\"fastqs,sample,library_type
 ${lines} \"\"\" > library.csv
-    sed -i \'\$ d\' library.csv # remove last empty line
+    sed -i -e \'\$ d\' library.csv # remove last empty line
     """
 }
diff --git a/modules/split_sheet/main.nf b/modules/split_sheet/main.nf
@@ -5,7 +5,7 @@ process SPLITSHEET {
     output:
         path "10X_Data.csv", emit: data
         path "Data.csv", emit: pipe_data, optional: true
-        path "FlexConfig_Data.csv", emit: flex, optional: true
+        path "10X_Flex_Data.csv", emit: flex, optional: true
         path "FeatureReference_Data.csv", emit: feature_reference, optional: true
     shell:
     '''

diff --git a/templates/manifest.html b/templates/manifest.html
@@ -83,7 +83,7 @@
     <div class="main-block">
       <div class="block-item">
         <h1><b>Nextflow manifest</b></h1>
-        <p> <b>Pipeline release:</b> 1.2.3</p>
+        <p> <b>Pipeline release:</b> 1.2.4</p>
         <p> <b>Subworkflow:</b> xxSubWorkflowxx</p>
         <p> <b> Maintainer:</b> [email protected]</p>
         <p> <b>Description:</b> Your data has been processed by the nextflow pipeline singleCellWorkflows. If you want more information on how your data was processed, follow the link below and navigate to your release!</p>