Merge pull request #186 from CDCgov/seqera_patch_kao

fixed channel mixup and removed remnants of utility function
CDCgov · Mar 15, 2024 · 4dc7bae · 4dc7bae
2 parents e8c3df2 + af898e4
commit 4dc7bae
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Showing 7 changed files with 9 additions and 48 deletions.
diff --git a/modules/local/liftoff_annotation/main.nf b/modules/local/liftoff_annotation/main.nf
diff --git a/modules/local/liftoff_cli_annotation/main.nf b/modules/local/liftoff_cli_annotation/main.nf
@@ -20,7 +20,7 @@ process LIFTOFF_CLI {
         }
 
 	input:
-	tuple val(meta), path(fasta)
+	tuple val(meta), path(fasta), path(fastq1), path(fastq2)
     path ref_fasta_path 
     path ref_gff_path 
 

diff --git a/modules/local/repeatmasker_annotation/main.nf b/modules/local/repeatmasker_annotation/main.nf
@@ -12,7 +12,7 @@ process REPEATMASKER {
         'quay.io/biocontainers/repeatmasker:4.1.5--pl5321hdfd78af_0'}"
 
 	input:
-	tuple val(meta), path(fasta_path)
+	tuple val(meta), path(fasta_path), path(fast1), path(fastq2)
 	path repeat_library
 
 	script:

diff --git a/modules/local/vadr_annotation/main.nf b/modules/local/vadr_annotation/main.nf
@@ -12,7 +12,7 @@ process VADR {
         'staphb/vadr:latest' : 'staphb/vadr:latest' }"
 
     input:
-	tuple val(meta), path(fasta_path)
+	tuple val(meta), path(fasta_path), path(fastq1), path(fastq2)
     path vadr_models_dir
 
     script:

diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf
@@ -18,9 +18,8 @@ process BAKTA {
     publishDir "$params.output_dir/$params.bakta_output_dir", mode: 'copy', overwrite: params.overwrite_output
 
     input:
-    val signal
     path db_path
-    tuple val(meta), path(fasta_path)
+    tuple val(meta), path(fasta_path), path(fastq1), path(fastq2)
 
     script:
     def args = task.ext.args  ?: ''

diff --git a/modules/nf-core/bakta/baktadbdownload/main.nf b/modules/nf-core/bakta/baktadbdownload/main.nf
@@ -6,8 +6,7 @@ process BAKTADBDOWNLOAD {
         'quay.io/biocontainers/bakta:1.8.2--pyhdfd78af_0' }"
 
     input: 
-    val signal
-
+
     output:
     path "bakta_db/*"           , emit: db
 

diff --git a/workflows/tostadas.nf b/workflows/tostadas.nf
@@ -79,6 +79,7 @@ workflow TOSTADAS {
 
     // Create initial submission channel
     submission_ch = metadata_ch.join(reads_ch)
+
     // check if the user wants to skip annotation or not
     if ( params.annotation ) {
         if ( params.virus && !params.bacteria ) {
@@ -87,7 +88,7 @@ workflow TOSTADAS {
             if ( params.repeatmasker_liftoff ) {
              // run repeatmasker annotation on files
                 REPEATMASKER_LIFTOFF (
-                    fasta_ch
+                    reads_ch
                 )
                 repeatmasker_gff_ch = REPEATMASKER_LIFTOFF.out.gff.collect().flatten()
                 .map { 
@@ -97,14 +98,13 @@ workflow TOSTADAS {
                 }
 
             // set up submission channels
-            // submission_ch = metadata_ch.join(fasta_ch)
             submission_ch = submission_ch.join(repeatmasker_gff_ch) // meta.id, fasta, fastq1, fastq2, gff
             }
 
             // run vadr processes
             if ( params.vadr ) {
                 RUN_VADR (
-                    fasta_ch
+                    reads_ch
                 )
                 vadr_gff_ch = RUN_VADR.out.gff
                     .collect()
@@ -121,7 +121,7 @@ workflow TOSTADAS {
         // run bakta annotation process
             if ( params.bakta == true ) {
                 RUN_BAKTA(
-                    fasta_ch
+                    reads_ch
                 )
                 // set up submission channels
                 bakta_gff_ch = RUN_BAKTA.out.gff3
@@ -130,7 +130,6 @@ workflow TOSTADAS {
                         meta = [id:it.getSimpleName()] 
                         [ meta, it ]
                     }
-                // submission_ch = metadata_ch.join(fasta_ch)
                 submission_ch = submission_ch.join(bakta_gff_ch) // meta.id, fasta, fastq1, fastq2, gff
             }   
         }
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,8 +6,7 @@ process BAKTADBDOWNLOAD { @@
             'quay.io/biocontainers/bakta:1.8.2--pyhdfd78af_0' }"
         input:
-        val signal
         output:
         path "bakta_db/*"           , emit: db
@@ Expand Down @@