Merge pull request #135 from replikation/fix134

Fix134
replikation · Jun 30, 2021 · 3f9d011 · 3f9d011
2 parents ad970dc + c6ac3fa
commit 3f9d011
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Showing 3 changed files with 7 additions and 3 deletions.
diff --git a/.github/workflows/DryRun.yml b/.github/workflows/DryRun.yml
@@ -25,3 +25,7 @@ jobs:
       run: |
           mkdir fast5 
           ./nextflow run poreCov.nf --fast5 fast5/  -stub -profile stub --cores 2 --max_cores 2
+    - name: fast5 dry run nanopolish
+      run: |
+          mkdir fast5_2 
+          ./nextflow run poreCov.nf --fast5 fast5_2/ --nanopolish  -stub -profile stub --cores 2 --max_cores 2
diff --git a/poreCov.nf b/poreCov.nf
@@ -118,7 +118,7 @@ if (params.fast5 == true) { exit 5, "Please provide a fast5 dir via [--fast5]" }
 if (params.minLength && !params.minLength.toString().matches("[0-9]+")) { exit 5, "Please provide an integer number (e.g. 300) as minimal read length via [--minLength]" }
 if (params.maxLength && !params.maxLength.toString().matches("[0-9]+")) { exit 5, "Please provide an integer number (e.g. 300) as maximum read length via [--maxLength]" }
 if (params.nanopolish == true && (params.fastq || params.fastq_pass) ) { exit 5, "Please provide sequencing_summary.txt via [--nanopolish]" }
-if (params.nanopolish && !params.fast5 ) { exit 5, "Please provide a fast5 dir for nanopolish [--fast5]" }
+if (!workflow.profile.contains('test_fast5')) { if (params.nanopolish && !params.fast5 ) { exit 5, "Please provide a fast5 dir for nanopolish [--fast5]" } }
 if (params.extended && !params.samples ) { exit 5, "When using --extended you need to specify also a sample.csv via [--samples]" }
 
 /************************** 

diff --git a/workflows/artic_nanopore_nCov19.nf b/workflows/artic_nanopore_nCov19.nf
@@ -51,7 +51,7 @@ workflow artic_ncov_np_wf {
 
         // plot amplicon coverage
         covarplot(
-            artic_medaka.out.covarplot.combine(external_primer_schemes)
+            artic_nanopolish.out.covarplot.combine(external_primer_schemes)
         )
 
         // error logging
@@ -60,4 +60,4 @@ workflow artic_ncov_np_wf {
     emit:   
         assembly
         filter_fastq_by_length.out
-}
+}