Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Rm copy_to_cron module #360

Merged
merged 1 commit into from
Oct 28, 2024
Merged

Rm copy_to_cron module #360

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Updated PRP to version 0.11.0
- Update `configs/nextflow.dev.config` root fpath
- Changed the freebayes output directory
- Remove `copy_to_cron` module

## [0.9.0]

Expand Down
7 changes: 2 additions & 5 deletions configs/nextflow.base.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -192,9 +192,6 @@ process {
withName: chewbbaca_split_results {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
}
withName: copy_to_cron {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/cron", mode: 'copy', overwrite: true, pattern: '*.json' ]
}
withName: create_analysis_result {
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
Expand All @@ -205,7 +202,7 @@ process {
}
withName: create_yaml {
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ]
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/jasen/${params.speciesDir}", mode: 'copy', overwrite: true ] ] : [])
ext.args_prp = {"${params.outdir}/${params.speciesDir}/analysis_result"}
ext.args_sourmash = {"${params.outdir}/${params.speciesDir}/sourmash"}
ext.args_ska = {"${params.outdir}/${params.speciesDir}/ska"}
Expand All @@ -215,7 +212,7 @@ process {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/emmtyper", mode: 'copy', overwrite: true ]
}
withName: export_to_cdm {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ]
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true ] ] : [])
}
withName: flye {
container = "${params.containerDir}/flye.sif"
Expand Down
5 changes: 1 addition & 4 deletions configs/nextflow.ci.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -181,9 +181,6 @@ process {
withName: chewbbaca_split_results {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
}
withName: copy_to_cron {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/cron", mode: 'copy', overwrite: true, pattern: '*.json' ]
}
withName: create_analysis_result {
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
Expand All @@ -194,7 +191,7 @@ process {
}
withName: create_yaml {
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ]
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/jasen/${params.speciesDir}", mode: 'copy', overwrite: true ] ] : [])
ext.args_prp = {"${params.outdir}/${params.speciesDir}/analysis_result"}
ext.args_sourmash = {"${params.outdir}/${params.speciesDir}/sourmash"}
ext.args_ska = {"${params.outdir}/${params.speciesDir}/ska"}
Expand Down
7 changes: 2 additions & 5 deletions configs/nextflow.dev.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -196,9 +196,6 @@ process {
withName: chewbbaca_split_results {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
}
withName: copy_to_cron {
publishDir = [ [ path: "/fs1/results/cron/jasen/${params.speciesDir}", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true, pattern: '*.cdmpy' ] ]
}
withName: create_analysis_result {
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
Expand All @@ -209,7 +206,7 @@ process {
}
withName: create_yaml {
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ]
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/jasen/${params.speciesDir}", mode: 'copy', overwrite: true ] ] : [])
ext.args_prp = {"${params.outdir}/${params.speciesDir}/analysis_result"}
ext.args_sourmash = {"${params.outdir}/${params.speciesDir}/sourmash"}
ext.args_ska = {"${params.outdir}/${params.speciesDir}/ska"}
Expand All @@ -219,7 +216,7 @@ process {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/emmtyper", mode: 'copy', overwrite: true ]
}
withName: export_to_cdm {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ]
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true ] ] : [])
}
withName: freebayes {
container = "https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hbfe0e7f_2"
Expand Down
8 changes: 3 additions & 5 deletions configs/nextflow.hopper.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,7 @@ profiles {
params.species = 'streptococcus pyogenes'
params.speciesDir = 'spyogenes'
params.mlstScheme = 'spyogenes'
params.symlinkDir = "/access/jasen/spyogenes/"
params.referenceGenome = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta"
params.referenceGenomeIdx = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta.fai"
params.referenceGenomeGff = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.gff"
Expand Down Expand Up @@ -195,9 +196,6 @@ process {
withName: chewbbaca_split_results {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
}
withName: copy_to_cron {
publishDir = [ [ path: "/fs1/results/cron/jasen/${params.speciesDir}", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true, pattern: '*.cdmpy' ] ]
}
withName: create_analysis_result {
container = "docker://clinicalgenomicslund/bonsai-prp:0.11.0"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
Expand All @@ -208,7 +206,7 @@ process {
}
withName: create_yaml {
container = "docker://clinicalgenomicslund/bonsai-prp:0.11.0"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ]
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/jasen/${params.speciesDir}", mode: 'copy', overwrite: true ] ] : [])
ext.args_prp = {"${params.outdir}/${params.speciesDir}/analysis_result"}
ext.args_sourmash = {"${params.outdir}/${params.speciesDir}/sourmash"}
ext.args_ska = {"${params.outdir}/${params.speciesDir}/ska"}
Expand All @@ -218,7 +216,7 @@ process {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/emmtyper", mode: 'copy', overwrite: true ]
}
withName: export_to_cdm {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ]
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true ] ] : [])
}
withName: flye {
container = "${params.containerDir}/flye.sif"
Expand Down
7 changes: 2 additions & 5 deletions configs/nextflow.ngp.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -205,9 +205,6 @@ process {
withName: chewbbaca_split_results {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
}
withName: copy_to_cron {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/cron", mode: 'copy', overwrite: true, pattern: '*.json' ]
}
withName: create_analysis_result {
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
Expand All @@ -218,7 +215,7 @@ process {
}
withName: create_yaml {
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ]
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/jasen/${params.speciesDir}", mode: 'copy', overwrite: true ] ] : [])
ext.args_prp = {"${params.outdir}/${params.speciesDir}/analysis_result"}
ext.args_sourmash = {"${params.outdir}/${params.speciesDir}/sourmash"}
ext.args_ska = {"${params.outdir}/${params.speciesDir}/ska"}
Expand All @@ -228,7 +225,7 @@ process {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/emmtyper", mode: 'copy', overwrite: true ]
}
withName: export_to_cdm {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ]
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true ] ] : [])
}
withName: freebayes {
cpus = params.cpus_small
Expand Down
29 changes: 0 additions & 29 deletions nextflow-modules/modules/cron/main.nf
View file
Open in desktop

This file was deleted.

6 changes: 1 addition & 5 deletions workflows/escherichia_coli.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ include { bwa_mem as bwa_mem_dedup } from '../nextflow-modules/
include { chewbbaca_allelecall } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { chewbbaca_create_batch_list } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { chewbbaca_split_results } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { copy_to_cron } from '../nextflow-modules/modules/cron/main.nf'
include { create_analysis_result } from '../nextflow-modules/modules/prp/main.nf'
include { create_cdm_input } from '../nextflow-modules/modules/prp/main.nf'
include { create_yaml } from '../nextflow-modules/modules/yaml/main.nf'
Expand Down Expand Up @@ -170,8 +169,6 @@ workflow CALL_ESCHERICHIA_COLI {

export_to_cdm(create_cdm_input.out.json.join(ch_seqrun_meta), params.speciesDir)

copy_to_cron(create_yaml.out.yaml.join(export_to_cdm.out.cdm))

ch_versions = ch_versions.mix(CALL_BACTERIAL_BASE.out.versions)
ch_versions = ch_versions.mix(amrfinderplus.out.versions)
ch_versions = ch_versions.mix(bwa_index.out.versions)
Expand All @@ -188,7 +185,6 @@ workflow CALL_ESCHERICHIA_COLI {
emit:
pipeline_result = create_analysis_result.out.json
cdm = export_to_cdm.out.cdm
cron_yaml = copy_to_cron.out.yaml
cron_cdm = copy_to_cron.out.cdm
yaml = create_yaml.out.yaml
versions = ch_versions
}
6 changes: 1 addition & 5 deletions workflows/klebsiella_pneumoniae.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ include { bwa_mem as bwa_mem_dedup } from '../nextflow-modules/
include { chewbbaca_allelecall } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { chewbbaca_create_batch_list } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { chewbbaca_split_results } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { copy_to_cron } from '../nextflow-modules/modules/cron/main.nf'
include { create_analysis_result } from '../nextflow-modules/modules/prp/main.nf'
include { create_cdm_input } from '../nextflow-modules/modules/prp/main.nf'
include { create_yaml } from '../nextflow-modules/modules/yaml/main.nf'
Expand Down Expand Up @@ -167,8 +166,6 @@ workflow CALL_KLEBSIELLA_PNEUMONIAE {

export_to_cdm(create_cdm_input.out.json.join(ch_seqrun_meta), params.speciesDir)

copy_to_cron(create_yaml.out.yaml.join(export_to_cdm.out.cdm))

ch_versions = ch_versions.mix(CALL_BACTERIAL_BASE.out.versions)
ch_versions = ch_versions.mix(amrfinderplus.out.versions)
ch_versions = ch_versions.mix(bwa_index.out.versions)
Expand All @@ -185,7 +182,6 @@ workflow CALL_KLEBSIELLA_PNEUMONIAE {
emit:
pipeline_result = create_analysis_result.out.json
cdm = export_to_cdm.out.cdm
cron_yaml = copy_to_cron.out.yaml
cron_cdm = copy_to_cron.out.cdm
yaml = create_yaml.out.yaml
versions = ch_versions
}
6 changes: 1 addition & 5 deletions workflows/mycobacterium_tuberculosis.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@ nextflow.enable.dsl=2
include { get_meta } from '../methods/get_meta.nf'
include { annotate_delly } from '../nextflow-modules/modules/prp/main.nf'
include { bracken } from '../nextflow-modules/modules/bracken/main.nf'
include { copy_to_cron } from '../nextflow-modules/modules/cron/main.nf'
include { create_analysis_result } from '../nextflow-modules/modules/prp/main.nf'
include { add_igv_track as add_variant_igv_track} from '../nextflow-modules/modules/prp/main.nf'
include { add_igv_track as add_locus_igv_track } from '../nextflow-modules/modules/prp/main.nf'
Expand Down Expand Up @@ -116,8 +115,6 @@ workflow CALL_MYCOBACTERIUM_TUBERCULOSIS {

export_to_cdm(create_cdm_input.out.json.join(ch_seqrun_meta), params.speciesDir)

copy_to_cron(create_yaml.out.yaml.join(export_to_cdm.out.cdm))

ch_versions = ch_versions.mix(CALL_BACTERIAL_BASE.out.versions)
ch_versions = ch_versions.mix(create_analysis_result.out.versions)
ch_versions = ch_versions.mix(mykrobe.out.versions)
Expand All @@ -127,7 +124,6 @@ workflow CALL_MYCOBACTERIUM_TUBERCULOSIS {
emit:
pipeline_result = add_locus_igv_track.out.json
cdm = export_to_cdm.out.cdm
cron_yaml = copy_to_cron.out.yaml
cron_cdm = copy_to_cron.out.cdm
yaml = create_yaml.out.yaml
versions = ch_versions
}
6 changes: 1 addition & 5 deletions workflows/staphylococcus_aureus.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ include { bwa_mem as bwa_mem_dedup } from '../nextflow-modules/
include { chewbbaca_allelecall } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { chewbbaca_create_batch_list } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { chewbbaca_split_results } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { copy_to_cron } from '../nextflow-modules/modules/cron/main.nf'
include { create_analysis_result } from '../nextflow-modules/modules/prp/main.nf'
include { create_cdm_input } from '../nextflow-modules/modules/prp/main.nf'
include { create_yaml } from '../nextflow-modules/modules/yaml/main.nf'
Expand Down Expand Up @@ -164,8 +163,6 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {

export_to_cdm(create_cdm_input.out.json.join(ch_seqrun_meta), params.speciesDir)

copy_to_cron(create_yaml.out.yaml.join(export_to_cdm.out.cdm))

ch_versions = ch_versions.mix(CALL_BACTERIAL_BASE.out.versions)
ch_versions = ch_versions.mix(amrfinderplus.out.versions)
ch_versions = ch_versions.mix(bwa_index.out.versions)
Expand All @@ -181,7 +178,6 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
emit:
pipeline_result = create_analysis_result.out.json
cdm = export_to_cdm.out.cdm
cron_yaml = copy_to_cron.out.yaml
cron_cdm = copy_to_cron.out.cdm
yaml = create_yaml.out.yaml
versions = ch_versions
}
6 changes: 1 addition & 5 deletions workflows/streptococcus.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ include { bwa_mem as bwa_mem_dedup } from '../nextflow-modules/
include { chewbbaca_allelecall } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { chewbbaca_create_batch_list } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { chewbbaca_split_results } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { copy_to_cron } from '../nextflow-modules/modules/cron/main.nf'
include { create_analysis_result } from '../nextflow-modules/modules/prp/main.nf'
include { create_cdm_input } from '../nextflow-modules/modules/prp/main.nf'
include { create_yaml } from '../nextflow-modules/modules/yaml/main.nf'
Expand Down Expand Up @@ -187,8 +186,6 @@ workflow CALL_STREPTOCOCCUS {

export_to_cdm(create_cdm_input.out.json.join(ch_seqrun_meta), speciesDir)

copy_to_cron(create_yaml.out.yaml.join(export_to_cdm.out.cdm))

ch_versions = ch_versions.mix(CALL_BACTERIAL_BASE.out.versions)
ch_versions = ch_versions.mix(amrfinderplus.out.versions)
ch_versions = ch_versions.mix(bracken.out.versions)
Expand All @@ -209,7 +206,6 @@ workflow CALL_STREPTOCOCCUS {
emit:
pipeline_result = create_analysis_result.out.json
cdm = export_to_cdm.out.cdm
cron_yaml = copy_to_cron.out.yaml
cron_cdm = copy_to_cron.out.cdm
yaml = create_yaml.out.yaml
versions = ch_versions
}
6 changes: 1 addition & 5 deletions workflows/streptococcus_pyogenes.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ include { bwa_mem as bwa_mem_dedup } from '../nextflow-modules/
include { chewbbaca_allelecall } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { chewbbaca_create_batch_list } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { chewbbaca_split_results } from '../nextflow-modules/modules/chewbbaca/main.nf'
include { copy_to_cron } from '../nextflow-modules/modules/cron/main.nf'
include { create_analysis_result } from '../nextflow-modules/modules/prp/main.nf'
include { create_cdm_input } from '../nextflow-modules/modules/prp/main.nf'
include { create_yaml } from '../nextflow-modules/modules/yaml/main.nf'
Expand Down Expand Up @@ -165,8 +164,6 @@ workflow CALL_STREPTOCOCCUS_PYOGENES {

export_to_cdm(create_cdm_input.out.json.join(ch_seqrun_meta), params.speciesDir)

copy_to_cron(create_yaml.out.yaml.join(export_to_cdm.out.cdm))

ch_versions = ch_versions.mix(CALL_BACTERIAL_BASE.out.versions)
ch_versions = ch_versions.mix(amrfinderplus.out.versions)
ch_versions = ch_versions.mix(bwa_index.out.versions)
Expand All @@ -182,7 +179,6 @@ workflow CALL_STREPTOCOCCUS_PYOGENES {
emit:
pipeline_result = create_analysis_result.out.json
cdm = export_to_cdm.out.cdm
cron_yaml = copy_to_cron.out.yaml
cron_cdm = copy_to_cron.out.cdm
yaml = create_yaml.out.yaml
versions = ch_versions
}
Loading