From c3fd3dfafb6f0e4eff4c81a4c5a064c0175ecbae Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Wed, 10 May 2023 15:55:09 +0200
Subject: [PATCH] hicstuff fragment & filter plot option correction
---
bin/hicstuff_filter.py | 13 ++++++++++---
bin/hicstuff_fragments.py | 8 ++++++++
conf/hicstuff.config | 10 +++++-----
modules/local/hicstuff/filter_event.nf | 1 +
modules/local/hicstuff/fragment_enzyme.nf | 1 +
5 files changed, 25 insertions(+), 8 deletions(-)
diff --git a/bin/hicstuff_filter.py b/bin/hicstuff_filter.py
index a06f9e6..23b7424 100755
--- a/bin/hicstuff_filter.py
+++ b/bin/hicstuff_filter.py
@@ -538,13 +538,20 @@ if __name__ == "__main__":
prefix = args.prefix
pairs_out = prefix+"_"+pairs_out
plot = args.plot
- plot.title()
- if plot == "False":
+ if plot.lower() == "false":
plot = False
- elif plot == "True":
+ elif plot.lower() == "true":
plot = True
dist_plot = args.dist_plot
+ if dist_plot == "None":
+ dist_plot = None
+ else:
+ dist_plot = prefix+"_"+dist_plot
pie_plot = args.pie_plot
+ if pie_plot == "None":
+ pie_plot = None
+ else:
+ pie_plot = prefix+"_"+pie_plot
uncut_thr, loop_thr = get_thresholds(
pairs_idx, plot_events=plot, fig_path=dist_plot, prefix=prefix
diff --git a/bin/hicstuff_fragments.py b/bin/hicstuff_fragments.py
index 489945d..5594097 100755
--- a/bin/hicstuff_fragments.py
+++ b/bin/hicstuff_fragments.py
@@ -19,9 +19,17 @@ if __name__ == "__main__":
index = args.index
min_size = args.min_size
circular = args.circular
+ if circular.lower() == "false":
+ circular = False
+ elif circular.lower() == "true":
+ circular = True
output_contigs = args.output_contigs
output_frags = args.output_frags
plot = args.plot
+ if plot.lower() == "false":
+ plot = False
+ elif plot.lower() == "true":
+ plot = True
fig_path = args.fig_path
diff --git a/conf/hicstuff.config b/conf/hicstuff.config
index a4e4be8..44f2782 100644
--- a/conf/hicstuff.config
+++ b/conf/hicstuff.config
@@ -121,10 +121,10 @@ params {
// Hicstuff
hicstuff_bwt2_align_opts = '--very-sensitive-local'
hicstuff_min_size = 0
- hicstuff_circular = 'False'
+ hicstuff_circular = 'frue'
hicstuff_output_contigs = 'info_contigs.txt'
hicstuff_output_frags = 'fragments_list.txt'
- hicstuff_frags_plot = 'False'
+ hicstuff_frags_plot = 'false'
hicstuff_frags_plot_path = 'frags_hist.pdf'
hicstuff_valid_pairs = 'valid.pairs'
hicstuff_valid_idx = 'valid_idx.pairs'
@@ -132,9 +132,9 @@ params {
hicstuff_matrix = 'abs_fragments_contacts_weighted.txt'
hicstuff_bin = 10000
hicstuff_valid_idx_filtered = 'valid_idx_filtered.pairs'
- hicstuff_plot_events = 'False'
- hicstuff_pie_plot = 'None'
- hicstuff_dist_plot = 'None'
+ hicstuff_plot_events = 'false'
+ hicstuff_pie_plot = 'distrib'
+ hicstuff_dist_plot = 'dist'
//Hicstuff optional modules
filter_event = true
diff --git a/modules/local/hicstuff/filter_event.nf b/modules/local/hicstuff/filter_event.nf
index bc45e87..2fa7051 100644
--- a/modules/local/hicstuff/filter_event.nf
+++ b/modules/local/hicstuff/filter_event.nf
@@ -10,6 +10,7 @@ process FILTER_EVENT {
output:
tuple val(meta1), path("*_valid_idx_filtered.pairs"), emit: idx_pairs_filtered
+ path("*.png"), optional: true
script:
diff --git a/modules/local/hicstuff/fragment_enzyme.nf b/modules/local/hicstuff/fragment_enzyme.nf
index d17fdfe..b770ee4 100644
--- a/modules/local/hicstuff/fragment_enzyme.nf
+++ b/modules/local/hicstuff/fragment_enzyme.nf
@@ -12,6 +12,7 @@ process FRAGMENT_ENZYME {
output:
tuple val(meta), path(params.hicstuff_output_contigs) , emit: info_contigs
tuple val(meta), path(params.hicstuff_output_frags), emit: fragments_list
+ path("*.pdf"), optional: true
script:
--
GitLab