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Dp24 jbrowse only #307

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merged 21 commits into from
Nov 15, 2024
Merged

Dp24 jbrowse only #307

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5882074
Adding new line
DLBPointon Jun 27, 2024
4ebc614
Merge branch 'main' of https://github.com/sanger-tol/treeval
DLBPointon Jul 4, 2024
42b846e
New workflow on request from GRIT, closes #305
DLBPointon Jul 12, 2024
b3bd2cd
Add support for new workflow
DLBPointon Jul 12, 2024
4210ca0
Testing arch to fix pretext
DLBPointon Jul 12, 2024
d3a98e3
Add support for new workflow
DLBPointon Jul 12, 2024
b82e921
Correction
DLBPointon Jul 12, 2024
e81653d
Correction
DLBPointon Jul 12, 2024
4af6d93
Added version output and removed the liberal use of spaces which are …
DLBPointon Jul 16, 2024
8c4b7b9
Remove dp24's liberal use of spaces - not very nf-core
DLBPointon Jul 18, 2024
5964920
added conda not available quotes to modules lacking conda envs closes…
DLBPointon Jul 18, 2024
70a771a
Fixes to modules
DLBPointon Jul 18, 2024
24bfc60
Fix variable
DLBPointon Jul 18, 2024
fc86857
Merge branch 'dev' into dp24_jbrowse_only
DLBPointon Nov 15, 2024
9fbbc11
Merged from main
DLBPointon Nov 15, 2024
4b0fc99
Updating container
DLBPointon Nov 15, 2024
dd8ac09
Another incorrect container
DLBPointon Nov 15, 2024
e6be044
Update main.nf
DLBPointon Nov 15, 2024
9e375d5
Update cram_filter_minimap2_filter5end_fixmate_sort.nf
DLBPointon Nov 15, 2024
6358ab3
Merge pull request #325 from sanger-tol/DLBPointon-patch-2
DLBPointon Nov 15, 2024
919a7f6
Merge pull request #326 from sanger-tol/DLBPointon-patch-1
DLBPointon Nov 15, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -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:
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14 changes: 14 additions & 0 deletions main.nf
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Expand Up @@ -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
Expand All @@ -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
Expand All @@ -68,6 +78,10 @@ workflow RAPID_TOL {
SANGERTOL_TREEVAL_RAPID_TOL ()
}

workflow JBROWSE {
SANGERTOL_TREEVAL_JBROWSE ()
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
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4 changes: 2 additions & 2 deletions modules/local/avgcov.nf
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Expand Up @@ -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)
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5 changes: 5 additions & 0 deletions modules/local/bamtobed_sort.nf
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Expand Up @@ -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)

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4 changes: 2 additions & 2 deletions modules/local/chunkfasta.nf
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Expand Up @@ -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')
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4 changes: 2 additions & 2 deletions modules/local/concatblocks.nf
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Expand Up @@ -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)
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5 changes: 5 additions & 0 deletions modules/local/cram_filter_align_bwamem2_fixmate_sort.nf
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Expand Up @@ -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)

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5 changes: 5 additions & 0 deletions modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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_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(ref), path(reference)

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4 changes: 2 additions & 2 deletions modules/local/extract_buscogene.nf
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Expand Up @@ -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:
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10 changes: 5 additions & 5 deletions modules/local/extract_cov_iden.nf
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Expand Up @@ -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"
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6 changes: 3 additions & 3 deletions modules/local/extract_repeat.nf
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Expand Up @@ -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
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12 changes: 6 additions & 6 deletions modules/local/extract_telo.nf
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Expand Up @@ -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}"
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11 changes: 8 additions & 3 deletions modules/local/find_telomere_regions.nf
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Expand Up @@ -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}"
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9 changes: 4 additions & 5 deletions modules/local/find_telomere_windows.nf
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Expand Up @@ -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}"
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13 changes: 9 additions & 4 deletions modules/local/fkutils/fkprof/main.nf
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Expand Up @@ -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 "FIND_TELOMERE_REGIONS 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 ?: ""
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10 changes: 5 additions & 5 deletions modules/local/gap_length.nf
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Expand Up @@ -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 ?: "${meta.id}"
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9 changes: 8 additions & 1 deletion modules/local/generate_cram_csv.nf
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Expand Up @@ -2,7 +2,14 @@ process GENERATE_CRAM_CSV {
tag "${meta.id}"
label 'process_tiny'

container 'quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1'
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'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)
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6 changes: 3 additions & 3 deletions modules/local/get_largest_scaff.nf
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Expand Up @@ -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
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10 changes: 5 additions & 5 deletions modules/local/get_paired_contact_bed.nf
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Expand Up @@ -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'
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10 changes: 5 additions & 5 deletions modules/local/getminmaxpunches.nf
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Expand Up @@ -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.
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9 changes: 8 additions & 1 deletion modules/local/graphoverallcoverage.nf
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Expand Up @@ -2,7 +2,14 @@ process GRAPHOVERALLCOVERAGE {
tag "$meta.id"
label "process_single"

container 'quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1'
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'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)
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3 changes: 1 addition & 2 deletions modules/local/juicer_tools_pre.nf
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Expand Up @@ -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' }"

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10 changes: 5 additions & 5 deletions modules/local/paf_to_bed.nf
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Expand Up @@ -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"
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