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Make outdir great again #73

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merged 1 commit into from
Jan 7, 2025
Merged

Make outdir great again #73

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111 changes: 83 additions & 28 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ process {

withName: 'IDENTIFY_SEQ_ONLINE|WRITE_SEQINFO' {
publishDir = [
path: { "${params.outdir}/seqinfo" },
path: { "${params.outdir}/seqinfo/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -35,7 +35,7 @@ process {

withName: 'FETCH_OMA_GROUP_LOCAL|FETCH_OMA_GROUP_ONLINE' {
publishDir = [
path: { "${params.outdir}/orthologs/oma" },
path: { "${params.outdir}/orthologs/${meta.id}/oma" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -46,7 +46,7 @@ process {

withName: 'FETCH_PANTHER_GROUP_LOCAL|FETCH_PANTHER_GROUP_ONLINE' {
publishDir = [
path: { "${params.outdir}/orthologs/panther" },
path: { "${params.outdir}/orthologs/${meta.id}/panther" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -57,7 +57,7 @@ process {

withName: 'FETCH_INSPECTOR_GROUP_ONLINE' {
publishDir = [
path: { "${params.outdir}/orthologs/orthoinspector" },
path: { "${params.outdir}/orthologs/${meta.id}/orthoinspector" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -68,7 +68,7 @@ process {

withName: 'FETCH_EGGNOG_GROUP_LOCAL|FETCH_EGGNOG_GROUP_ONLINE' {
publishDir = [
path: { "${params.outdir}/orthologs/eggnog" },
path: { "${params.outdir}/orthologs/${meta.id}/eggnog" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -83,7 +83,7 @@ process {

withName: 'SPLIT_ID_FORMAT' {
publishDir = [
path: { "${params.outdir}/sequences" },
path: { "${params.outdir}/sequences/${meta.id}/" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -92,7 +92,7 @@ process {

withName: 'FETCH_UNIPROT_SEQUENCES' {
publishDir = [
path: { "${params.outdir}/sequences" },
path: { "${params.outdir}/sequences/${meta.id}/uniprot" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -110,7 +110,7 @@ process {

withName: 'FETCH_ENSEMBL_SEQUENCES' {
publishDir = [
path: { "${params.outdir}/sequences" },
path: { "${params.outdir}/sequences/${meta.id}/ensembl" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -119,7 +119,7 @@ process {

withName: 'FETCH_REFSEQ_SEQUENCES' {
publishDir = [
path: { "${params.outdir}/sequences" },
path: { "${params.outdir}/sequences/${meta.id}/refseq" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -128,16 +128,17 @@ process {

withName: 'FETCH_OMA_SEQUENCES' {
publishDir = [
path: { "${params.outdir}/sequences" },
path: { "${params.outdir}/sequences/${meta.id}/oma" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
]
}

withName: 'CONCAT_FASTA' {
ext.prefix = { "${meta.id}_orthologs.txt" }
publishDir = [
path: { "${params.outdir}/sequences" },
path: { "${params.outdir}/sequences/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -146,7 +147,7 @@ process {
withName: 'CONCAT_HITS' {
ext.prefix = {"${meta.id}_hits.txt"}
publishDir = [
path: { "${params.outdir}/sequences" },
path: { "${params.outdir}/sequences/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -156,7 +157,7 @@ process {
withName: 'CONCAT_MISSES' {
ext.prefix = {"${meta.id}_misses.txt"}
publishDir = [
path: { "${params.outdir}/sequences" },
path: { "${params.outdir}/sequences/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -168,7 +169,7 @@ process {
ext.prefix = {"${meta.id}_ids"}
ext.suffix = "txt"
publishDir = [
path: { "${params.outdir}/merge" },
path: { "${params.outdir}/merge/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -179,11 +180,40 @@ process {
// ID merging
// ----------------------

withName: 'SPLIT_TAXIDS' {
publishDir = [
path: { "${params.outdir}/merge/${meta.id}/taxids" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
]
}

withName: 'MERGE_FASTA_IDS' {
ext.prefix = { "${meta.id}_ids_raw" }
publishDir = [
path: { "${params.outdir}/merge/${meta.id}/" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
]
}

withName: 'DIAMOND_CLUSTER' {
ext.args = "--approx-id 90"
ext.prefix = { "${meta.id}_${db.toString().tokenize(".")[0].tokenize("_")[-1]}" }
ext.prefix = { "${meta.id}_${db.toString().tokenize(".")[0].tokenize("_")[-1]}_clusters" }
publishDir = [
path: { "${params.outdir}/merge" },
path: { "${params.outdir}/merge/${meta.id}/clusters" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
]
}

withName: 'MERGE_DIAMOND' {
ext.prefix = { "${meta.id}_pairs_raw.txt" }
publishDir = [
path: { "${params.outdir}/merge/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -201,10 +231,10 @@ process {
print col1[1];
}
}\'"""
ext.prefix = { "${meta.id}_ids_diamond" }
ext.prefix = { "${meta.id}_pairs_clean" }
ext.suffix = "txt"
publishDir = [
path: { "${params.outdir}/merge" },
path: { "${params.outdir}/merge/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -216,7 +246,17 @@ process {
ext.prefix = { "${meta.id}_clusters" }
ext.suffix = "txt"
publishDir = [
path: { "${params.outdir}/merge" },
path: { "${params.outdir}/merge/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
]
}

withName: 'MERGE_ALL' {
ext.prefix = { "${meta.id}_idmap_raw.tsv" }
publishDir = [
path: { "${params.outdir}/merge/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -226,13 +266,19 @@ process {
withName: 'REDUCE_IDMAP' {
ext.args = "-F\'\t\'"
ext.args2 = "\'NF >= 2\'"
ext.prefix = { "${meta.id}_idmap" }
ext.prefix = { "${meta.id}_idmap.tsv" }
publishDir = [
path: { "${params.outdir}/merge/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
]
}

withName: 'MERGE_CSV' {
ext.args = '-f 1 --outer-join --na 0'
publishDir = [
path: { "${params.outdir}/orthologs/merge_csv" },
path: { "${params.outdir}/score/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -245,15 +291,15 @@ process {

withName: 'MAKE_SCORE_TABLE' {
publishDir = [
path: { "${params.outdir}/orthologs/score_table" },
path: { "${params.outdir}/score/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'FILTER_HITS' {
publishDir = [
path: { "${params.outdir}/orthologs/filter_hits" },
path: { "${params.outdir}/score/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -262,15 +308,15 @@ process {

withName: 'PLOT_ORTHOLOGS' {
publishDir = [
path: { "${params.outdir}/orthologs/plots" },
path: { "${params.outdir}/score/${meta.id}/plots" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'MAKE_HITS_TABLE' {
publishDir = [
path: { "${params.outdir}/orthologs/stats" },
path: { "${params.outdir}/score/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -281,15 +327,24 @@ process {
ext.args = "-u 0 -k"
ext.prefix = "aggregated_hits"
publishDir = [
path: { "${params.outdir}/orthologs/stats" },
path: { "${params.outdir}/score" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'MAKE_STATS' {
publishDir = [
path: { "${params.outdir}/orthologs/stats" },
path: { "${params.outdir}/score/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
]
}

withName: 'STATS2CSV' {
publishDir = [
path: { "${params.outdir}/score/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.output_intermediates
Expand All @@ -300,7 +355,7 @@ process {
ext.args = "-u NA"
ext.prefix = "aggregated_stats"
publishDir = [
path: { "${params.outdir}/orthologs/stats" },
path: { "${params.outdir}/score" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand Down
15 changes: 7 additions & 8 deletions modules/local/make_report.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,8 @@ process MAKE_REPORT {
tuple val(meta), path(id), path(taxid), path(exact), path(score_table), path(filtered_hits), path(support_plot), path(venn_plot), path(jaccard_plot), path(orthostats), path(seq_hits), path(seq_misses), path(params_file)

output:
tuple val(meta), path("*dist/*"), emit: report_files
path "versions.yml" , emit: versions
tuple val(meta), path("${prefix}/*"), emit: report_files
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -20,7 +20,7 @@ process MAKE_REPORT {
error("Local MAKE_REPORT module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

def prefix = task.ext.prefix ?: meta.id
prefix = task.ext.prefix ?: meta.id
seqhits_cmd = seq_hits ? "cp $seq_hits public/seq_hits.txt" : ''
seqmisses_cmd = seq_misses ? "cp $seq_misses public/seq_misses.txt" : ''
"""
Expand Down Expand Up @@ -50,8 +50,8 @@ process MAKE_REPORT {
echo "python3 -m http.server 0" > dist/run.sh
chmod u+x dist/run.sh

# add prefix to directory name
mv dist ${prefix}_dist
# change output directory name
mv dist ${prefix}

cat <<- END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -62,10 +62,9 @@ process MAKE_REPORT {
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir ${prefix}_dist
touch ${prefix}_dist/${prefix}_run.sh
mkdir ${prefix}
touch ${prefix}/run.sh

cat <<- END_VERSIONS > versions.yml
${task.process}:
Expand Down
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