Merge branch 'dev' into master

nextflow.config

@@ -233,14 +233,13 @@ env {
 }
 
 // Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
-"""
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o pipefail" // Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false

workflows/crisprseq_screening.nf

@@ -126,14 +126,15 @@ workflow CRISPRSEQ_SCREENING {
             BOWTIE2_ALIGN (
             ch_input,
             BOWTIE2_BUILD.out.index,
+            ch_fasta,
             false,
             false
             )
 
             ch_versions = ch_versions.mix(BOWTIE2_ALIGN.out.versions)
 
 
-            BOWTIE2_ALIGN.out.aligned.map{ meta, bam ->
+            BOWTIE2_ALIGN.out.bam.map{ meta, bam ->
                 [meta, [bam]]
             }.set{ch_input}
         }

workflows/crisprseq_targeted.nf

@@ -602,10 +602,11 @@ workflow CRISPRSEQ_TARGETED {
         BOWTIE2_ALIGN (
             ch_preprocess_reads,
             BOWTIE2_BUILD.out.index,
+            ch_oriented_reference,
             false,
             true
         )
-        ch_mapped_bam = BOWTIE2_ALIGN.out.aligned
+        ch_mapped_bam = BOWTIE2_ALIGN.out.bam
         ch_versions = ch_versions.mix(BOWTIE2_ALIGN.out.versions)
     }