Linting for the strict syntax

.github/workflows/sanger_test.yml

@@ -7,21 +7,26 @@ jobs:
     name: Run LSF tests
     runs-on: ubuntu-latest
     steps:
+      - name: Sets env vars for workflow_dispatch
+        run: |
+          echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV
+        if: github.event_name == 'workflow_dispatch'
+
       - name: Launch workflow via tower
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ github.sha }}
+          revision: ${{ env.REVISION }}
+          workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }}
           parameters: |
             {
-              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ github.sha }}",
+              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}",
+              "use_work_dir_as_temp": true,
             }
           profiles: test,sanger,singularity,cleanup
-
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: |

.github/workflows/sanger_test_full.yml

@@ -34,8 +34,7 @@ jobs:
               "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}",
             }
           profiles: test_full,sanger,singularity,cleanup
-
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: |

conf/base.config

@@ -11,10 +11,10 @@ process {
     maxErrors     = '-1'
 
     // Most of the pipeline requires very little resources
-    cpus   = 1
+    cpus          = 1
     // but still gradually increase the resources to allow the pipeline to self-heal
-    memory = { 50.MB * task.attempt }
-    time   = { 30.min * task.attempt }
+    memory        = { 50.MB * task.attempt }
+    time          = { 30.min * task.attempt }
 
     // tabix needs pointers to the sequences in memory
     withName: '.*:.*:FASTA_WINDOWS:TABIX_TABIX_.*' {
@@ -23,7 +23,7 @@ process {
     }
 
     // fasta_windows takes more memory on larger genomes
-    withName: 'FASTAWINDOWS' {
+    withName: FASTAWINDOWS {
         // 1 CPU per 1 Gbp
         cpus   = { Math.ceil(fasta.size() / 1000000000) }
         // 100 MB per 45 Mbp

conf/modules.config

@@ -16,18 +16,17 @@ process {
         publishDir = [
             path: { "${meta.outdir}/${meta.analysis_subdir}" },
             mode: 'copy',
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
-    withName: 'TABIX_BGZIP' {
+    withName: TABIX_BGZIP {
         ext.args = "-i"
     }
-    withName: 'TABIX_TABIX_CSI' {
+    withName: TABIX_TABIX_CSI {
         ext.args = "--preset bed --csi"
     }
-    withName: 'TABIX_TABIX_TBI' {
+    withName: TABIX_TABIX_TBI {
         ext.args = "--preset bed"
     }
-
 }

conf/test.config

@@ -14,7 +14,7 @@ process {
     resourceLimits = [
         cpus: 4,
         memory: '15.GB',
-        time: '1.h'
+        time: '1.h',
     ]
 }
 
@@ -23,5 +23,5 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    fasta  = 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/927/399/515/GCA_927399515.1_gfLaeSulp1.1/GCA_927399515.1_gfLaeSulp1.1_genomic.fna.gz'
+    fasta                      = 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/927/399/515/GCA_927399515.1_gfLaeSulp1.1/GCA_927399515.1_gfLaeSulp1.1_genomic.fna.gz'
 }

conf/test_full.config

@@ -15,5 +15,5 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = "${projectDir}/assets/samplesheet.csv"
+    input                      = "${projectDir}/assets/samplesheet.csv"
 }

main.nf

@@ -26,7 +26,6 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_sequ
 // WORKFLOW: Run main analysis pipeline depending on type of input
 //
 workflow SANGERTOL_SEQUENCECOMPOSITION {
-
     take:
     samplesheet // channel: samplesheet read in from --input
 
@@ -35,7 +34,7 @@ workflow SANGERTOL_SEQUENCECOMPOSITION {
     //
     // WORKFLOW: Run pipeline
     //
-    SEQUENCECOMPOSITION (
+    SEQUENCECOMPOSITION(
         samplesheet
     )
 }
@@ -46,12 +45,10 @@ workflow SANGERTOL_SEQUENCECOMPOSITION {
 */
 
 workflow {
-
-    main:
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
-    PIPELINE_INITIALISATION (
+    PIPELINE_INITIALISATION(
         params.version,
         params.validate_params,
         params.monochrome_logs,
@@ -60,19 +57,20 @@ workflow {
         params.input,
         params.help,
         params.help_full,
-        params.show_hidden
+        params.show_hidden,
+        params.fasta,
     )
 
     //
     // WORKFLOW: Run main workflow
     //
-    SANGERTOL_SEQUENCECOMPOSITION (
+    SANGERTOL_SEQUENCECOMPOSITION(
         PIPELINE_INITIALISATION.out.samplesheet
     )
     //
     // SUBWORKFLOW: Run completion tasks
     //
-    PIPELINE_COMPLETION (
+    PIPELINE_COMPLETION(
         params.email,
         params.email_on_fail,
         params.plaintext_email,

modules/local/extract_column.nf

@@ -1,27 +1,27 @@
 process EXTRACT_COLUMN {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "conda-forge::python=3.9.1"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'biocontainers/python:3.9--1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/python:3.9--1'
+        : 'biocontainers/python:3.9--1'}"
 
     input:
     tuple val(meta), path(tsv)
-    val(column_number)
+    val column_number
 
     output:
     tuple val(meta), path("*.bedGraph"), emit: bedgraph
-    path "versions.yml"                , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    cut -f1-3,$column_number $tsv | tail -n +2 > ${prefix}.bedGraph
+    cut -f1-3,${column_number} ${tsv} | tail -n +2 > ${prefix}.bedGraph
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":