Merge pull request #72 from cidgoh/dev

Squashed some bugs and added automation to the genomics group
cidgoh · Oct 9, 2024 · 3c48b98 · 3c48b98
2 parents ebdae81 + 0c0620d
commit 3c48b98
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Showing 4 changed files with 41 additions and 5 deletions.
diff --git a/.github/workflows/notify-slack-on-release.yml b/.github/workflows/notify-slack-on-release.yml
@@ -0,0 +1,18 @@
+name: Notify Slack on New Release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  notify:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Send notification to Slack
+        env:
+          SLACK_WEBHOOK_URL: ${{ secrets.CIDGOH_SLACK_WEBHOOK }}
+        run: |
+          curl -X POST -H 'Content-type: application/json' --data \
+          '{"text":"A new release has been published: <${{ github.event.release.html_url }}|${{ github.event.release.tag_name }}> by *${{ github.event.release.author.login }}*.\n\n*Release Notes:* \n${{ github.event.release.body }}"}' \
+          $SLACK_WEBHOOK_URL
diff --git a/subworkflows/local/plasmids.nf b/subworkflows/local/plasmids.nf
@@ -7,6 +7,8 @@ workflow PLASMIDS {
     take:
         genome
     main:
+        ch_plasmidfinder_fa = Channel.empty()
+        ch_mobsuite_fa = Channel.empty()
 
         // inititalize version channel
         ch_versions = Channel.empty()

diff --git a/subworkflows/local/seqqc.nf b/subworkflows/local/seqqc.nf
@@ -97,19 +97,15 @@ workflow SEQQC {
     // SUBWORKFLOW: Read in samplesheet, validate and stage input files
     //
 
-
     ch_input
         .branch {
             illumina : it[0].mode == 'illumina'
             nanopore : it[0].mode == 'nanopore'
         }
         .set {ch_raw_reads}
 
-
-
     CAT_NANOPORE_FASTQ(ch_raw_reads.nanopore)
     ch_reads_merged = CAT_NANOPORE_FASTQ.out.reads
-    //ch_versions = ch_versions.mix(CAT_NANOPORE_FASTQ.out.versions)
     ch_reads = ch_reads.mix(ch_raw_reads.illumina).mix(ch_reads_merged)
 
     //

diff --git a/workflows/bacpaq.nf b/workflows/bacpaq.nf
@@ -12,7 +12,12 @@ ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.mu
 ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
 //ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
 */
-
+def convertEmptyToNull = { value ->
+    if (value.toString().trim().isEmpty() || (value instanceof List && value.isEmpty())) {
+        return null
+    }
+    return value
+}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -43,6 +48,9 @@ workflow BACPAQ {
     ch_multiqc_files = Channel.empty()
 
     ch_illumina = samplesheet
+        .map { meta, fastq_1, fastq_2, fastq_dir, genome ->
+            [meta, convertEmptyToNull(fastq_1), fastq_2, fastq_dir, genome]
+        }
         .filter { meta, fastq_1, fastq_2, fastq_dir, genome ->
             fastq_1 != null
         }
@@ -53,14 +61,26 @@ workflow BACPAQ {
                 return [ [ id:meta.id, single_end: false, mode:'illumina' ], [fastq_1, fastq_2 ]]
             }
         }
+    ch_illumina.ifEmpty {
+        log.warn "No Illumina samples found in the samplesheet, skipping Illumina-specifc processes."
+    }
     ch_onp = samplesheet
+        .map { meta, fastq_1, fastq_2, fastq_dir, genome ->
+            [meta, fastq_1, fastq_2, convertEmptyToNull(fastq_dir), genome]
+        }
         .filter { meta, fastq_1, fastq_2, fastq_dir, genome ->
             fastq_dir != null
         }
         .map {  meta, fastq_1, fastq_2, fastq_dir, genome ->
                 return [ [ id:meta.id, single_end: true, mode:'nanopore' ], [fastq_dir ]]
         }
+    ch_onp.ifEmpty {
+        log.warn "No Nanopore samples found in the samplesheet, skipping Nanopore-specifc processes."
+    }
     ch_genome = samplesheet
+        .map { meta, fastq_1, fastq_2, fastq_dir, genome ->
+            [meta, fastq_1, fastq_2, fastq_dir, convertEmptyToNull(genome)]
+        }
         .filter { meta, fastq_1, fastq_2, fastq_dir, genome ->
             genome != null
         }