Merge with dp24_jbrowse_only

sanger-tol · Nov 15, 2024 · 35d9f23 · 35d9f23
2 parents 8407bfc + 919a7f6
commit 35d9f23
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -22,7 +22,7 @@ jobs:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'sanger-tol/treeval') }}"
-    runs-on: ubuntu2204-8c
+    runs-on: [ubuntu-latest] # Let's see if Pretext errors are a architecture thing
     strategy:
       matrix:
         NXF_VER:

diff --git a/main.nf b/main.nf
@@ -25,6 +25,7 @@ WorkflowMain.initialise( workflow, params, log )
 include { TREEVAL           } from './workflows/treeval'
 include { TREEVAL_RAPID     } from './workflows/treeval_rapid'
 include { TREEVAL_RAPID_TOL } from './workflows/treeval_rapid_tol'
+include { TREEVAL_JBROWSE   } from './workflows/treeval_jbrowse'
 
 //
 // WORKFLOW: RUN MAIN PIPELINE GENERATING ALL OUTPUT
@@ -47,6 +48,15 @@ workflow SANGERTOL_TREEVAL_RAPID_TOL {
         TREEVAL_RAPID_TOL ()
 }
 
+//
+// WORKFLOW: RUN ONLY THE SUBWORKFLOWS REQUIRED FOR JBROWSE UPLOAD
+//              - THIS IS TO COMPLEMENT A NEW PROCESS WHERE MAJORITY OF TICKETS WILL BE RC
+//                  AND GET REQUESTED FOR FULL
+//
+workflow SANGERTOL_TREEVAL_JBROWSE {
+    TREEVAL_JBROWSE ()
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     RUN ALL WORKFLOWS
@@ -68,6 +78,10 @@ workflow RAPID_TOL {
         SANGERTOL_TREEVAL_RAPID_TOL ()
 }
 
+workflow JBROWSE {
+    SANGERTOL_TREEVAL_JBROWSE ()
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END

diff --git a/modules/local/avgcov.nf b/modules/local/avgcov.nf
@@ -4,8 +4,8 @@ process AVGCOV {
 
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'docker.io/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(bedfile)

diff --git a/modules/local/bamtobed_sort.nf b/modules/local/bamtobed_sort.nf
@@ -6,6 +6,11 @@ process BAMTOBED_SORT {
         'https://depot.galaxyproject.org/singularity/mulled-v2-9d3a458f6420e5712103ae2af82c94d26d63f059:60b54b43045e8cf39ba307fd683c69d4c57240ce-0' :
         'biocontainers/mulled-v2-9d3a458f6420e5712103ae2af82c94d26d63f059:60b54b43045e8cf39ba307fd683c69d4c57240ce-0' }"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "BAMTOBED_SORT module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     input:
     tuple val(meta), path(bam)
 

diff --git a/modules/local/chunkfasta.nf b/modules/local/chunkfasta.nf
@@ -4,8 +4,8 @@ process CHUNKFASTA {
 
     conda "conda-forge::pyfasta=0.5.2-1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/pyfasta:0.5.2--py_1' :
-    'biocontainers/pyfasta:0.5.2--py_1' }"
+        'https://depot.galaxyproject.org/singularity/pyfasta:0.5.2--py_1' :
+        'biocontainers/pyfasta:0.5.2--py_1' }"
 
     input:
     tuple val(meta), path('input.fasta')

diff --git a/modules/local/concatblocks.nf b/modules/local/concatblocks.nf
@@ -4,8 +4,8 @@ process CONCATBLOCKS {
 
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-            'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-            'docker.io/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(mergeblocks)

diff --git a/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf b/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf
@@ -6,6 +6,11 @@ process CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
         'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' :
         'biocontainers/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' }"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     input:
     tuple val(meta), path(cramfile), path(cramindex), val(from), val(to), val(base), val(chunkid), val(rglines), val(bwaprefix), path(reference)
 

diff --git a/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf b/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf
@@ -6,6 +6,11 @@ process CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT {
         'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' :
         'biocontainers/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' }"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     input:
     tuple val(meta), path(cramfile), path(cramindex), val(from), val(to), val(base), val(chunkid), val(rglines), val(ref), path(reference)
 

diff --git a/modules/local/extract_buscogene.nf b/modules/local/extract_buscogene.nf
@@ -4,8 +4,8 @@ process EXTRACT_BUSCOGENE {
 
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'docker.io/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'docker.io/ubuntu:20.04' }"
 
 
     input:

diff --git a/modules/local/extract_cov_iden.nf b/modules/local/extract_cov_iden.nf
@@ -4,15 +4,15 @@ process EXTRACT_COV_IDEN {
 
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'docker.io/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
-    tuple val( meta ), file( "*.bed" )  , emit: punchlist
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), file("*.bed")  , emit: punchlist
+    path "versions.yml"             , emit: versions
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}_${meta.type}_punchlist"

diff --git a/modules/local/extract_repeat.nf b/modules/local/extract_repeat.nf
@@ -8,11 +8,11 @@ process EXTRACT_REPEAT {
         'biocontainers/perl:5.26.2' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
-    tuple val( meta ), path( "*.bed" )  , emit: bed
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), path("*.bed")  , emit: bed
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/extract_telo.nf b/modules/local/extract_telo.nf
@@ -4,16 +4,16 @@ process EXTRACT_TELO {
 
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'docker.io/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
-    tuple val( meta ), file( "*bed" )   , emit: bed
-    tuple val( meta ), file("*bedgraph"), emit: bedgraph
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), file("*bed")     , emit: bed
+    tuple val(meta), file("*bedgraph"), emit: bedgraph
+    path "versions.yml"               , emit: versions
 
     shell:
     def prefix  = task.ext.prefix ?: "${meta.id}"

diff --git a/modules/local/find_telomere_regions.nf b/modules/local/find_telomere_regions.nf
@@ -4,13 +4,18 @@ process FIND_TELOMERE_REGIONS {
 
     container 'docker.io/library/gcc:10.4.0'
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "FIND_TELOMERE_REGIONS module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
     val (telomereseq)
 
     output:
-    tuple val( meta ), file( "*.telomere" ) , emit: telomere
-    path "versions.yml"                     , emit: versions
+    tuple val(meta), file("*.telomere") , emit: telomere
+    path "versions.yml"                 , emit: versions
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"

diff --git a/modules/local/find_telomere_windows.nf b/modules/local/find_telomere_windows.nf
@@ -3,17 +3,16 @@ process FIND_TELOMERE_WINDOWS {
     label 'process_low'
 
     conda "bioconda::java-jdk=8.0.112"
-    container "${ workflow.containerEngine == 'singularity' &&
-                    !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/java-jdk:8.0.112--1' :
         'biocontainers/java-jdk:8.0.112--1' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
-    tuple val( meta ), file( "*.windows" ) , emit: windows
-    path "versions.yml"                    , emit: versions
+    tuple val(meta), file("*.windows") , emit: windows
+    path "versions.yml"                , emit: versions
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"

diff --git a/modules/local/fkutils/fkprof/main.nf b/modules/local/fkutils/fkprof/main.nf
@@ -6,13 +6,18 @@ process FKUTILS_FKPROF {
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
     'docker.io/ubuntu:20.04' }"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "FKUTILS_FKPROF module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     input:
-    tuple val( meta ), path( reference )
-    tuple val( meta2 ), path( ktab )
+    tuple val(meta), path(reference)
+    tuple val(meta2), path(ktab)
 
     output:
-    tuple val( meta ), file( "*bed" ),  emit: bed
-    path "versions.yml",                emit: versions
+    tuple val(meta), file("*bed"),  emit: bed
+    path "versions.yml",            emit: versions
 
     script:
     def args    = task.ext.args     ?: ""

diff --git a/modules/local/gap_length.nf b/modules/local/gap_length.nf
@@ -4,15 +4,15 @@ process GAP_LENGTH {
 
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'docker.io/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
-    tuple val( meta ), file( "*bedgraph" )  , emit: bedgraph
-    path "versions.yml"                     , emit: versions
+    tuple val(meta), file("*bedgraph")  , emit: bedgraph
+    path "versions.yml"                 , emit: versions
 
     shell:
     def prefix = task.ext.prefix ?: "${meta.id}"

diff --git a/modules/local/generate_cram_csv.nf b/modules/local/generate_cram_csv.nf
@@ -6,6 +6,11 @@ process GENERATE_CRAM_CSV {
         'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' :
         'biocontainers/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' }"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "GENERATE_CRAM_CSV module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     input:
     tuple val(meta), path(crampath)
 

diff --git a/modules/local/get_largest_scaff.nf b/modules/local/get_largest_scaff.nf
@@ -5,11 +5,11 @@ process GET_LARGEST_SCAFF {
 
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'docker.io/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
     env largest_scaff   , emit: scaff_size

diff --git a/modules/local/get_paired_contact_bed.nf b/modules/local/get_paired_contact_bed.nf
@@ -4,15 +4,15 @@ process GET_PAIRED_CONTACT_BED {
 
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'docker.io/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
-    tuple val( meta ), file( "*bed" )   , emit: bed
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), file("*bed")   , emit: bed
+    path "versions.yml"             , emit: versions
 
     script:
     def pulled = '-T sort_tmp'

diff --git a/modules/local/getminmaxpunches.nf b/modules/local/getminmaxpunches.nf
@@ -4,16 +4,16 @@ process GETMINMAXPUNCHES{
 
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'docker.io/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(bedfile)
 
     output:
-    tuple val(meta), path ( '*zero.bed' )   , optional: true    , emit: min
-    tuple val(meta), path ( '*max.bed' )    , optional: true    , emit: max
-    path "versions.yml"                     , emit: versions
+    tuple val(meta), path ('*zero.bed')   , optional: true    , emit: min
+    tuple val(meta), path ('*max.bed')    , optional: true    , emit: max
+    path "versions.yml"                   , emit: versions
 
     shell:
     def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

diff --git a/modules/local/graphoverallcoverage.nf b/modules/local/graphoverallcoverage.nf
@@ -6,6 +6,11 @@ process GRAPHOVERALLCOVERAGE {
         'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' :
         'biocontainers/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' }"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "GRAPHOVERALLCOVERAGE module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     input:
     tuple val(meta), path(bed)
 

diff --git a/modules/local/juicer_tools_pre.nf b/modules/local/juicer_tools_pre.nf
@@ -5,8 +5,7 @@ process JUICER_TOOLS_PRE {
     label 'process_medium'
 
     conda "bioconda::java-jdk=8.0.112"
-    container "${ workflow.containerEngine == 'singularity' &&
-                    !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/java-jdk:8.0.112--1' :
         'biocontainers/java-jdk:8.0.112--1' }"
 

diff --git a/modules/local/paf_to_bed.nf b/modules/local/paf_to_bed.nf
@@ -4,15 +4,15 @@ process PAF2BED {
 
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'docker.io/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
-    tuple val( meta ), file( "*_punchlist.bed" ), emit: punchlist
-    path "versions.yml"                         , emit: versions
+    tuple val(meta), file("*_punchlist.bed"), emit: punchlist
+    path "versions.yml"                     , emit: versions
 
     script:
     def prefix  = task.ext.prefix ?: "${meta.id}_${meta.type}_punchlist"