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Updating yaml assignments and formatting, closes #168
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DLBPointon committed Nov 21, 2023
1 parent b63db57 commit 0e84c79
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Showing 3 changed files with 19 additions and 22 deletions.
14 changes: 7 additions & 7 deletions subworkflows/local/hic_mapping.nf
Original file line number Diff line number Diff line change
Expand Up @@ -30,14 +30,14 @@ workflow HIC_MAPPING {
take:
reference_tuple // Channel [ val(meta), path(file) ]
reference_index // Channel [ val(meta), path(file) ]
dot_genome // Channel [ val(meta), [ datafile ]]
dot_genome // Channel [ val(meta), [ datafile ] ]
hic_reads_path // Channel [ val(meta), path(directory) ]
gap_file
coverage_file
logcoverage_file
telo_file
repeat_density_file
workflow_setting // val( {RAPID | FULL } )
gap_file // Channel [ val(meta), path(file) ]
coverage_file // Channel [ val(meta), path(file) ]
logcoverage_file // Channel [ val(meta), path(file) ]
telo_file // Channel [ val(meta), path(file) ]
repeat_density_file // Channel [ val(meta), path(file) ]
workflow_setting // val( { RAPID | FULL } )

main:
ch_versions = Channel.empty()
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1 change: 0 additions & 1 deletion workflows/treeval.nf
Original file line number Diff line number Diff line change
Expand Up @@ -238,7 +238,6 @@ workflow TREEVAL {
GENERATE_GENOME.out.ref_index,
GENERATE_GENOME.out.dot_genome,
YAML_INPUT.out.hic_reads,
YAML_INPUT.out.assembly_id,
GAP_FINDER.out.gap_file,
LONGREAD_COVERAGE.out.ch_covbw_nor,
LONGREAD_COVERAGE.out.ch_covbw_log,
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26 changes: 12 additions & 14 deletions workflows/treeval_rapid.nf
Original file line number Diff line number Diff line change
Expand Up @@ -64,67 +64,65 @@ workflow TREEVAL_RAPID {
// SUBWORKFLOW: Takes input fasta file and sample ID to generate a my.genome file
//
GENERATE_GENOME (
YAML_INPUT.out.assembly_id,
YAML_INPUT.out.reference
)
ch_versions = ch_versions.mix(GENERATE_GENOME.out.versions)
ch_versions = ch_versions.mix( GENERATE_GENOME.out.versions )

//
// SUBWORKFLOW: GENERATES A BIGWIG FOR A REPEAT DENSITY TRACK
//
REPEAT_DENSITY (
GENERATE_GENOME.out.reference_tuple,
YAML_INPUT.out.reference,
GENERATE_GENOME.out.dot_genome
)
ch_versions = ch_versions.mix(REPEAT_DENSITY.out.versions)
ch_versions = ch_versions.mix( REPEAT_DENSITY.out.versions )

//
// SUBWORKFLOW: GENERATES A GAP.BED FILE TO ID THE LOCATIONS OF GAPS
//
GAP_FINDER (
GENERATE_GENOME.out.reference_tuple,
YAML_INPUT.out.reference,
GENERATE_GENOME.out.max_scaff_size
)
ch_versions = ch_versions.mix(GAP_FINDER.out.versions)
ch_versions = ch_versions.mix( GAP_FINDER.out.versions )

//
// SUBWORKFLOW: GENERATE TELOMERE WINDOW FILES WITH PACBIO READS AND REFERENCE
//
TELO_FINDER (
GENERATE_GENOME.out.max_scaff_size,
GENERATE_GENOME.out.reference_tuple,
YAML_INPUT.out.reference,
YAML_INPUT.out.teloseq
)
ch_versions = ch_versions.mix(TELO_FINDER.out.versions)
ch_versions = ch_versions.mix( TELO_FINDER.out.versions )

//
// SUBWORKFLOW: Takes reference, pacbio reads
//
LONGREAD_COVERAGE (
GENERATE_GENOME.out.reference_tuple,
YAML_INPUT.out.reference,
GENERATE_GENOME.out.dot_genome,
YAML_INPUT.out.pacbio_reads
)
ch_versions = ch_versions.mix(LONGREAD_COVERAGE.out.versions)
ch_versions = ch_versions.mix( LONGREAD_COVERAGE.out.versions )

//
// SUBWORKFLOW: Takes reads and assembly, produces kmer plot
//
KMER (
GENERATE_GENOME.out.reference_tuple,
YAML_INPUT.out.reference,
YAML_INPUT.out.pacbio_reads
)
ch_versions = ch_versions.mix(KMER.out.versions)
ch_versions = ch_versions.mix( KMER.out.versions )

//
// SUBWORKFLOW: GENERATE HIC MAPPING TO GENERATE PRETEXT FILES AND JUICEBOX
//
HIC_MAPPING (
GENERATE_GENOME.out.reference_tuple,
YAML_INPUT.out.reference,
GENERATE_GENOME.out.ref_index,
GENERATE_GENOME.out.dot_genome,
YAML_INPUT.out.hic_reads,
YAML_INPUT.out.assembly_id,
GAP_FINDER.out.gap_file,
LONGREAD_COVERAGE.out.ch_covbw_nor,
LONGREAD_COVERAGE.out.ch_covbw_log,
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