Fixed reporting error when only one group (5d1573bc) · Commits · Chaos / Cutandrun

bin/lib/reports.py

+10 −7

Original line number	Diff line number	Diff line
		@@ -108,6 +108,7 @@ class Reports:
		self.metadata_table['spikein_alignment_rate'] = self.metadata_table.loc[:, ('bt2_total_aligned_spikein')] / self.metadata_table.loc[:, ('bt2_total_reads_spikein')] * 100

		# Change to percentage
		if 'frip' in self.metadata_noctrl_table.columns:
		self.metadata_noctrl_table['frip'] = self.metadata_noctrl_table['frip'] * 100

		def load_raw_frag_histogram(self):
		@@ -292,11 +293,13 @@ class Reports:
		data["06_02_peak_widths"] = data7b

		# Plot 7c
		if 'peak_repro' in self.metadata_noctrl_table.columns:
		plot7c, data7c = self.reproduced_peaks()
		plots["06_03_reproduced_peaks"] = plot7c
		data["06_03_reproduced_peaks"] = data7c

		# Plot 7d
		if 'frip' in self.metadata_noctrl_table.columns:
		plot7d, data7d = self.frags_in_peaks()
		plots["06_04_frags_in_peaks"] = plot7d
		data["06_04_frags_in_peaks"] = data7d

+4 −2

Original line number	Diff line number	Diff line
		@@ -26,10 +26,12 @@ process GENERATE_REPORTS {
		path '*frag_len_mqc.yaml', emit: frag_len_multiqc
		path '*.version.txt', emit: version

		script: // This script is bundled with the pipeline, in nf-core/cutandrun/bin/
		script:
		def meta_data_resolved = meta_data ? meta_data : meta_data_ctrl

		"""
		reporting.py gen_reports \\
		--meta $meta_data \\
		--meta $meta_data_resolved \\
		--meta_ctrl $meta_data_ctrl \\
		--raw_frag "*.frag_len.txt" \\
		--bin_frag "*bin500.awk.bed" \\

+4 −4

Original line number	Diff line number	Diff line
		@@ -987,7 +987,7 @@ workflow CUTANDRUN {
		* MODULE: Export meta-data to csv file
		*/
		EXPORT_META (
		ch_samtools_bam.collect{it[0]}.ifEmpty(["{NO-DATA}"]),
		ch_samtools_bam.collect{it[0]},
		"meta_table"
		)

		@@ -995,7 +995,7 @@ workflow CUTANDRUN {
		* MODULE: Export meta-data to csv file
		*/
		EXPORT_META_CTRL (
		ch_samtools_bam_ctrl.collect{it[0]}.ifEmpty(["{NO-DATA}"]),
		ch_samtools_bam_ctrl.collect{it[0]},
		"meta_table_ctrl"
		)

		@@ -1003,7 +1003,7 @@ workflow CUTANDRUN {
		* MODULE: Generate python reporting using mixture of meta-data and direct file processing
		*/
		GENERATE_REPORTS(
		EXPORT_META.out.csv, // meta-data report stats
		EXPORT_META.out.csv.collect().ifEmpty([]), // meta-data report stats
		EXPORT_META_CTRL.out.csv, // meta-data report stats
		SAMTOOLS_CUSTOMVIEW.out.tsv.collect{it[1]}, // raw fragments
		AWK_FRAG_BIN.out.file.collect{it[1]}, // binned fragments