Fix yml ver (#756)

* Fix kallisto index tests

* Fix nanoplot

* Fix kallistobustools

* Fix pairix

* Fix plasmidid

* Fix pbccs

* Fix raxmlng

* Fix prokka

* Fix shovill

* Fix typo

* Deleted workflow by mistake added again

modules/kallisto/index/main.nf

@@ -36,7 +36,7 @@ process KALLISTO_INDEX {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(kallisto 2>&1 | sed 's/^kallisto //; s/Usage.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//')
     END_VERSIONS
     """
 }

modules/kallisto/index/meta.yml

@@ -1,7 +1,7 @@
 name: kallisto_index
-description: write your description here
+description: Create kallisto index
 keywords:
-  - sort
+  - index
 tools:
   - kallisto:
       description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

modules/kallistobustools/count/main.nf

@@ -53,7 +53,7 @@ process KALLISTOBUSTOOLS_COUNT {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
     END_VERSIONS
     """
 }

modules/kallistobustools/ref/main.nf

@@ -47,7 +47,7 @@ process KALLISTOBUSTOOLS_REF {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
         END_VERSIONS
         """
     } else {
@@ -66,7 +66,7 @@ process KALLISTOBUSTOOLS_REF {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
         END_VERSIONS
         """
     }

modules/nanoplot/main.nf

@@ -39,7 +39,7 @@ process NANOPLOT {
         $input_file
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(NanoPlot --version 2>&1 | sed 's/^.*NanoPlot //; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/pairix/main.nf

@@ -34,7 +34,7 @@ process PAIRIX {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(pairix --help 2>&1 | sed 's/^.*Version: //; s/Usage.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(pairix --help 2>&1) | sed 's/^.*Version: //; s/Usage.*\$//')
     END_VERSIONS
     """
 }

modules/pbccs/main.nf

@@ -51,7 +51,7 @@ process PBCCS {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(ccs --version 2>&1 | grep -e 'commit')
+        ${getSoftwareName(task.process)}: \$(echo \$(ccs --version 2>&1) | grep 'ccs' | sed 's/^.*ccs //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/plasmidid/main.nf

@@ -47,7 +47,7 @@ process PLASMIDID {
     mv NO_GROUP/$prefix ./$prefix
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(plasmidID --version 2>&1)
+        ${getSoftwareName(task.process)}: \$(echo \$(plasmidID --version 2>&1))
     END_VERSIONS
     """
 }

modules/raxmlng/main.nf

@@ -36,7 +36,7 @@ process RAXMLNG {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(raxml-ng --version 2>&1 | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
     END_VERSIONS
     """
 }

tests/modules/kallisto/index/main.nf

@@ -7,7 +7,7 @@ include { KALLISTO_INDEX } from '../../../../modules/kallisto/index/main.nf' add
 workflow test_kallisto_index {
 
     def input = []
-    input = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     KALLISTO_INDEX ( input )
 }

tests/modules/kallistobustools/count/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf' addParams( options: [args:"--cellranger"] )
+include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf' addParams( options: [args:"--cellranger -m 1"] )
 
 workflow test_kallistobustools_count {
 

tests/modules/kallistobustools/ref/main.nf

@@ -30,3 +30,4 @@ workflow test_kallistobustools_ref_nucleus {
 
     KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
 }
+

tests/modules/plasmidid/test.yml

@@ -12,7 +12,6 @@
     - path: output/plasmidid/test/data/test.fna
       md5sum: 503a5e1d4654bb2df19420e211070db3
     - path: output/plasmidid/test/data/test.gbk
-      md5sum: c851bba9da6ec72cce591617067df50b
     - path: output/plasmidid/test/data/test.gff
       md5sum: 3ed8912ee9b0712ca491fa78ff5f4da1
     - path: output/plasmidid/test/data/test.karyotype_individual.txt
@@ -28,7 +27,6 @@
     - path: output/plasmidid/test/database/test.fna
       md5sum: 6b843fe652b4369addb382f61952c3dd
     - path: output/plasmidid/test/database/test.gbk
-      md5sum: 1f7972ecbb868823727157d2c482700d
     - path: output/plasmidid/test/database/test.gff
       md5sum: 7e65da147d0a413020b0d92b7b03ffcd
     - path: output/plasmidid/test/fasta_files/MT192765.1_term.fasta