diff --git a/bin/hicstuff_filter.py b/bin/hicstuff_filter.py index a06f9e6bca2f446c18f05a07e588cf72d51a9ee2..23b74245b8440ab3bbca398618f405d629f3d610 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 489945dd01948e200fc6b2ca48e4beafeee5b86f..5594097f4a8177d32ab879b75d9c18c6f814ee2d 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 a4e4be8129795a9287655ac5d1c15b609a2559f1..44f278270a317810d95f74d772194e9ddc7977a6 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 bc45e871bf6be0c25283d63a711f9508bd5fbba3..2fa70512ed1a815d50d61a4b8e3ba35d6eb748b6 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 d17fdfee3e6411555584309b0c6daee14e823c7e..b770ee4b8af0b3914b7e8541ff5002bf260fcd84 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: