Merge pull request #67 from nf-core/initial-release-review-changes

Apply the fourth set of reviewer recommendations
nf-core · Jul 17, 2024 · b9ed09e · b9ed09e
2 parents 2f86f87 + feca359
commit b9ed09e
Show file tree

Hide file tree

Showing 14 changed files with 25 additions and 34 deletions.
diff --git a/main.nf b/main.nf
@@ -80,7 +80,8 @@ workflow NFCORE_ONCOANALYSER {
     } else if (run_mode === Constants.RunMode.TARGETED) {
         TARGETED()
     } else {
-        assert false
+        log.error("received bad run mode: ${run_mode}")
+        Nextflow.exit(1)
     }
 
 }

diff --git a/modules/local/linx/visualiser/main.nf b/modules/local/linx/visualiser/main.nf
@@ -29,7 +29,7 @@ process LINX_VISUALISER {
     # used in the plot directory to force FusionFS to create the directory as ORANGE will treat the placeholder as a PNG
     # and fail. Optional outputs are possible but requires further channel logic and output to detect when complete.
     # Instead I place the two plot output directories under a parent directory, only operating on that to allow use of a
-    # placeholder and support empty outputs when using FusionFS. Handing missing/non-existent directories are deferred
+    # placeholder and support empty outputs when using FusionFS. Handling missing/non-existent directories are deferred
     # to downstream processes, bypassing the need to implement further channel operations.
 
     mkdir -p plots/

diff --git a/modules/local/svprep/assemble/main.nf b/modules/local/svprep/assemble/main.nf
@@ -9,12 +9,12 @@ process GRIDSS_ASSEMBLE {
 
     input:
     tuple val(meta), path(bams), path(bams_filtered), path(preprocess_dirs), val(labels)
-    path gridss_config
     path genome_fasta
     path genome_fai
     path genome_dict
     path genome_gridss_index
     path blocklist
+    path gridss_config
 
     output:
     tuple val(meta), path('gridss_assemble/'), emit: assemble_dir
@@ -44,7 +44,7 @@ process GRIDSS_ASSEMBLE {
 
     """
     # Create shadow directory with file symlinks of GRIDSS 'working' dir to prevent cache invalidation
-    # NOTE: for reasons that elude me, NF doesn't always stage in the workingdir; remove if it is present
+    # NOTE(SW): for reasons that elude me, NF doesn't always stage in the workingdir; remove if it is present
     shadow_input_directory() {
         src=\${1}
         dst="${output_dirname}/work/\${src##*/}"

diff --git a/modules/local/svprep/assemble/meta.yml b/modules/local/svprep/assemble/meta.yml
@@ -27,9 +27,6 @@ input:
   - labels:
       type: list
       description: List of labels corresponding to BAMs and GRIDSS preprocess output directories
-  - gridss_config:
-      type: file
-      description: GRIDSS configuration file (optional)
   - genome_fasta:
       type: file
       description: Reference genome assembly FASTA file
@@ -50,6 +47,9 @@ input:
       type: file
       description: GRIDSS blocklist file
       pattern: "*.{bed.gz}"
+  - gridss_config:
+      type: file
+      description: GRIDSS configuration file (optional)
 output:
   - meta:
       type: map

diff --git a/modules/local/svprep/call/main.nf b/modules/local/svprep/call/main.nf
@@ -9,12 +9,12 @@ process GRIDSS_CALL {
 
     input:
     tuple val(meta), path(bams), path(bams_filtered), path(assemble_dir), val(labels)
-    path gridss_config
     path genome_fasta
     path genome_fai
     path genome_dict
     path genome_gridss_index
     path blocklist
+    path gridss_config
 
     output:
     tuple val(meta), path('gridss_call/sv.svprep.gridss.vcf.gz'), emit: vcf
@@ -44,7 +44,7 @@ process GRIDSS_CALL {
 
     """
     # Create shadow directory with file symlinks of GRIDSS 'working' dir to prevent cache invalidation
-    # NOTE: for reasons that elude me, NF doesn't always stage in the workingdir; remove if it is present
+    # NOTE(SW): for reasons that elude me, NF doesn't always stage in the workingdir; remove if it is present
     shadow_input_directory() {
         src=\${1}
         dst="${output_dirname}/"

diff --git a/modules/local/svprep/call/meta.yml b/modules/local/svprep/call/meta.yml
@@ -27,9 +27,6 @@ input:
   - labels:
       type: list
       description: List of labels corresponding to BAMs and GRIDSS preprocess output directories
-  - gridss_config:
-      type: file
-      description: GRIDSS configuration file (optional)
   - genome_fasta:
       type: file
       description: Reference genome assembly FASTA file
@@ -50,6 +47,9 @@ input:
       type: file
       description: GRIDSS blocklist file
       pattern: "*.{bed.gz}"
+  - gridss_config:
+      type: file
+      description: GRIDSS configuration file (optional)
 output:
   - meta:
       type: map

diff --git a/modules/local/svprep/preprocess/main.nf b/modules/local/svprep/preprocess/main.nf
@@ -9,11 +9,11 @@ process GRIDSS_PREPROCESS {
 
     input:
     tuple val(meta), path(bam), path(bam_filtered)
-    path gridss_config
     path genome_fasta
     path genome_fai
     path genome_dict
     path genome_gridss_index
+    path gridss_config
 
     output:
     tuple val(meta), path("gridss_preprocess/${meta.sample_id}.sv_prep.sorted.bam.gridss.working/"), emit: preprocess_dir

diff --git a/modules/local/svprep/preprocess/meta.yml b/modules/local/svprep/preprocess/meta.yml
@@ -23,9 +23,6 @@ input:
       type: file
       description: Filtered BAM file
       pattern: "*.{bam}"
-  - gridss_config:
-      type: file
-      description: GRIDSS configuration file (optional)
   - genome_fasta:
       type: file
       description: Reference genome assembly FASTA file
@@ -42,6 +39,9 @@ input:
       type: file
       description: Reference genome assembly GRIDSS index file
       pattern: "*.{gridsscache}"
+  - gridss_config:
+      type: file
+      description: GRIDSS configuration file (optional)
 output:
   - meta:
       type: map

diff --git a/modules/local/virusbreakend/main.nf b/modules/local/virusbreakend/main.nf
@@ -9,12 +9,12 @@ process VIRUSBREAKEND {
 
     input:
     tuple val(meta), path(bam)
-    path gridss_config
     path genome_fasta
     path genome_fai
     path genome_dict
     path genome_gridss_index
     path virusbreakenddb
+    path gridss_config
 
     output:
     tuple val(meta), path("*.summary.tsv"), emit: tsv

diff --git a/modules/local/virusbreakend/meta.yml b/modules/local/virusbreakend/meta.yml
@@ -19,9 +19,6 @@ input:
       type: file
       description: BAM file
       pattern: "*.{bam}"
-  - gridss_config:
-      type: file
-      description: GRIDSS configuration file (optional)
   - genome_fasta:
       type: file
       description: Reference genome assembly FASTA file
@@ -41,6 +38,9 @@ input:
   - virusbreakenddb:
       type: directory
       description: VIRUSBreakend database directory
+  - gridss_config:
+      type: file
+      description: GRIDSS configuration file (optional)
 output:
   - meta:
       type: map

diff --git a/subworkflows/local/gridss_svprep_calling/main.nf b/subworkflows/local/gridss_svprep_calling/main.nf
@@ -184,11 +184,11 @@ workflow GRIDSS_SVPREP_CALLING {
     // Run process
     PREPROCESS(
         ch_preprocess_inputs,
-        gridss_config,
         genome_fasta,
         genome_fai,
         genome_dict,
         genome_gridss_index,
+        gridss_config,
     )
 
     ch_versions = ch_versions.mix(PREPROCESS.out.versions)
@@ -262,12 +262,12 @@ workflow GRIDSS_SVPREP_CALLING {
     // Run process
     ASSEMBLE(
         ch_assemble_inputs,
-        gridss_config,
         genome_fasta,
         genome_fai,
         genome_dict,
         genome_gridss_index,
         gridss_blocklist,
+        gridss_config,
     )
 
     ch_versions = ch_versions.mix(ASSEMBLE.out.versions)
@@ -292,12 +292,12 @@ workflow GRIDSS_SVPREP_CALLING {
     // Run process
     CALL(
         ch_call_inputs,
-        gridss_config,
         genome_fasta,
         genome_fai,
         genome_dict,
         genome_gridss_index,
         gridss_blocklist,
+        gridss_config,
     )
 
     ch_versions = ch_versions.mix(CALL.out.versions)

diff --git a/subworkflows/local/read_alignment_dna/main.nf b/subworkflows/local/read_alignment_dna/main.nf
@@ -134,12 +134,7 @@ workflow READ_ALIGNMENT_DNA {
 
             def meta_bwamem2 = [
                 *:meta_fastq_ready,
-
-
-                // TODO(SW): understand target format
                 read_group: "${meta_fastq_ready.sample_id}.${meta_fastq_ready.library_id}.${meta_fastq_ready.lane}",
-
-
             ]
 
             return [meta_bwamem2, fastq_fwd, fastq_rev]

diff --git a/subworkflows/local/read_alignment_rna/main.nf b/subworkflows/local/read_alignment_rna/main.nf
@@ -63,12 +63,7 @@ workflow READ_ALIGNMENT_RNA {
         .map { meta_fastq, fastq_fwd, fastq_rev ->
             def meta_star = [
                 *:meta_fastq,
-
-
-                // TODO(SW): understand target format
                 read_group: "${meta_fastq.sample_id}.${meta_fastq.library_id}.${meta_fastq.lane}",
-
-
             ]
 
             return [meta_star, fastq_fwd, fastq_rev]

diff --git a/subworkflows/local/virusbreakend_calling/main.nf b/subworkflows/local/virusbreakend_calling/main.nf
@@ -71,12 +71,12 @@ workflow VIRUSBREAKEND_CALLING {
     // Run process
     VIRUSBREAKEND(
         ch_virusbreakend_inputs,
-        gridss_config,
         genome_fasta,
         genome_fai,
         genome_dict,
         genome_gridss_index,
         virusbreakenddb,
+        gridss_config,
     )
 
     ch_versions = ch_versions.mix(VIRUSBREAKEND.out.versions)