From c85adfeb52d4df98defacc79b75a20f9730041d4 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Thu, 22 Feb 2024 14:33:08 +0100
Subject: [PATCH] connect hicstuff sub to cooler subworkflow
---
subworkflows/local/hicstuff.nf | 14 +++++++++++---
workflows/hic.nf | 32 +++++++++++++++++---------------
2 files changed, 28 insertions(+), 18 deletions(-)
diff --git a/subworkflows/local/hicstuff.nf b/subworkflows/local/hicstuff.nf
index 018360b..facd680 100644
--- a/subworkflows/local/hicstuff.nf
+++ b/subworkflows/local/hicstuff.nf
@@ -118,6 +118,7 @@ workflow HICSTUFF {
fasta.collect()
)
BAM2PAIRS.out.idx_pairs.set{ ch_idx_pairs }
+ BAM2PAIRS.out.valid_pairs.set{ ch_valid_pairs }
if( params.filter_event ){
FILTER_EVENT(
@@ -143,6 +144,12 @@ workflow HICSTUFF {
FILTER_PCR.out.idx_pairs_pcrfree.set{ ch_idx_pairs }
}
+ ch_idx_pairs.combine(ch_valid_pairs)
+ .map {
+ meta1, idx, meta2, pairs ->
+ meta1 == meta2 ? [ meta1, idx, pairs ] : null
+ }.set{ ch_pairs }
+
BUILD_MATRIX(
ch_idx_pairs,
FRAGMENT_ENZYME.out.fragments_list.collect()
@@ -153,12 +160,13 @@ workflow HICSTUFF {
FRAGMENT_ENZYME.out.fragments_list.collect()
)
- BUILD_MATRIX_COOL_ALT(
+ /* BUILD_MATRIX_COOL_ALT(
chromosome_size.collect(),
ch_idx_pairs
- )
+ ) */
emit:
- cool = BUILD_MATRIX_COOL_ALT.out.matrix
+ //cool = BUILD_MATRIX_COOL_ALT.out.matrix
+ pairs = ch_pairs
versions = ch_versions
}
diff --git a/workflows/hic.nf b/workflows/hic.nf
index f1cd351..6c3487e 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -222,14 +222,30 @@ workflow HIC {
ch_map_res,
ch_fasta
)
+ ch_pairs = HICPRO.out.pairs
ch_mqc = HICPRO.out.mqc
ch_versions = ch_versions.mix(HICPRO.out.versions)
+ }
+ else {
+ HICSTUFF(
+ ch_reads,
+ PREPARE_GENOME.out.index,
+ ch_ligation_site,
+ params.digestion, //str enzyme
+ ch_fasta,
+ PREPARE_GENOME.out.chromosome_size
+ )
+ //ch_cool = HICSTUFF.out.cool
+ ch_pairs = HICSTUFF.out.pairs
+ ch_mqc = Channel.empty()
+ ch_versions = ch_versions.mix(HICSTUFF.out.versions)
+ }
//
// SUB-WORKFLOW: COOLER
//
COOLER (
- HICPRO.out.pairs,
+ ch_pairs,
PREPARE_GENOME.out.chromosome_size,
ch_map_res
)
@@ -251,21 +267,7 @@ workflow HIC {
ch_versions = ch_versions.mix(HIC_PLOT_DIST_VS_COUNTS.out.versions)
}
ch_cool = COOLER.out.cool
-}
- else {
- HICSTUFF(
- ch_reads,
- PREPARE_GENOME.out.index,
- ch_ligation_site,
- params.digestion, //str enzyme
- ch_fasta,
- PREPARE_GENOME.out.chromosome_size
- )
- ch_cool = HICSTUFF.out.cool
- ch_mqc = Channel.empty()
- ch_versions = ch_versions.mix(HICSTUFF.out.versions)
- }
//
// MODULE: HICEXPLORER/HIC_PLOT_MATRIX
--
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