Loading .github/workflows/ci.yml +22 −9 Original line number Diff line number Diff line Loading @@ -146,21 +146,34 @@ jobs: matrix: nxf_version: ['21.10.3', ''] tags: - params - samplesheet - verify_output_input - verify_output_peak_calling - verify_output_reporting - verify_output_save - verify_output_skip - verify_output_align_only_q_filter - verify_output_align_duplicates_mark - verify_output_align_duplicates_remove - verify_output_align_duplicates_remove_target - verify_output_save_ref - verify_output_only_input - verify_output_save_merged - verify_output_skip_fastqc - verify_output_save_trimmed - verify_output_skip_trimming - verify_output_align_intermed - verify_output_align_only_align - verify_output_align_save_spikein_align - verify_output_align_save_unaligned - verify_output_only_filtering - verify_output_align_duplicates_mark - verify_output_align_duplicates_remove - verify_output_align_duplicates_remove_target - verify_output_peak_calling_only_peak_calling - test_bam_scale_none - test_bam_scale_spikein - test_bam_scale_cpm - test_bam_scale_rpkm - test_bam_scale_bpm - test_bam_scale_cpm_iggscale - test_peak_callers - test_conseneus_peaks_group - test_conseneus_peaks_all - test_conseneus_peaks_invalid - verify_output_reporting steps: - uses: actions/checkout@v2 Loading CHANGELOG.md +3 −3 Original line number Diff line number Diff line Loading @@ -57,6 +57,6 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi |------------|-------------|-------------| | `samtools` | 1.13 | 1.14 | > **NB:** Dependency has been __updated__ if both old and new version information is present. > **NB:** Dependency has been __added__ if just the new version information is present. > **NB:** Dependency has been __removed__ if version information isn't present. > **NB:** Dependency has been **updated** if both old and new version information is present. > **NB:** Dependency has been **added** if just the new version information is present. > **NB:** Dependency has been **removed** if version information isn't present. assets/multiqc_config.yaml +2 −2 Original line number Diff line number Diff line Loading @@ -37,11 +37,11 @@ module_order: - bowtie2: name: 'Bowtie2 (target)' path_filters: - "./bowtie2/*target.bowtie2.log" - "./bowtie2/*.bowtie2.log" - bowtie2: name: 'Bowtie2 (spike-in)' path_filters: - "./bowtie2/*spikein.bowtie2.log" - "./bowtie2_spikein/*.bowtie2.log" - samtools - picard - custom_content Loading bin/lib/reports.py +10 −4 Original line number Diff line number Diff line Loading @@ -99,10 +99,15 @@ class Reports: self.metadata_noctrl_table = pd.read_csv(self.meta_path, sep=',') self.metadata_table = pd.read_csv(self.meta_ctrl_path, sep=',') self.duplicate_info = False if 'dedup_percent_duplication' in self.metadata_table.columns: self.duplicate_info = True self.scale_factor_info = False if 'scale_factor' in self.metadata_table.columns: self.scale_factor_info = True # Make new perctenage alignment columns self.metadata_table['target_alignment_rate'] = self.metadata_table.loc[:, ('bt2_total_aligned_target')] / self.metadata_table.loc[:, ('bt2_total_reads_target')] * 100 self.metadata_table['spikein_alignment_rate'] = self.metadata_table.loc[:, ('bt2_total_aligned_spikein')] / self.metadata_table.loc[:, ('bt2_total_reads_spikein')] * 100 Loading Loading @@ -303,6 +308,7 @@ class Reports: data["04_replicate_heatmap"] = data5 # Plot section 6 if self.scale_factor_info == True: multi_plot, data6 = self.scale_factor_summary() plots["05_01_scale_factor"] = multi_plot[0] plots["05_02_frag_count"] = multi_plot[1] Loading conf/base.config +3 −3 Original line number Diff line number Diff line Loading @@ -45,7 +45,7 @@ process { errorStrategy = 'retry' maxRetries = 2 } withName:CUSTOM_DUMPSOFTWAREVERSIONS { cache = false } // withName:CUSTOM_DUMPSOFTWAREVERSIONS { // cache = false // } } Loading
.github/workflows/ci.yml +22 −9 Original line number Diff line number Diff line Loading @@ -146,21 +146,34 @@ jobs: matrix: nxf_version: ['21.10.3', ''] tags: - params - samplesheet - verify_output_input - verify_output_peak_calling - verify_output_reporting - verify_output_save - verify_output_skip - verify_output_align_only_q_filter - verify_output_align_duplicates_mark - verify_output_align_duplicates_remove - verify_output_align_duplicates_remove_target - verify_output_save_ref - verify_output_only_input - verify_output_save_merged - verify_output_skip_fastqc - verify_output_save_trimmed - verify_output_skip_trimming - verify_output_align_intermed - verify_output_align_only_align - verify_output_align_save_spikein_align - verify_output_align_save_unaligned - verify_output_only_filtering - verify_output_align_duplicates_mark - verify_output_align_duplicates_remove - verify_output_align_duplicates_remove_target - verify_output_peak_calling_only_peak_calling - test_bam_scale_none - test_bam_scale_spikein - test_bam_scale_cpm - test_bam_scale_rpkm - test_bam_scale_bpm - test_bam_scale_cpm_iggscale - test_peak_callers - test_conseneus_peaks_group - test_conseneus_peaks_all - test_conseneus_peaks_invalid - verify_output_reporting steps: - uses: actions/checkout@v2 Loading
CHANGELOG.md +3 −3 Original line number Diff line number Diff line Loading @@ -57,6 +57,6 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi |------------|-------------|-------------| | `samtools` | 1.13 | 1.14 | > **NB:** Dependency has been __updated__ if both old and new version information is present. > **NB:** Dependency has been __added__ if just the new version information is present. > **NB:** Dependency has been __removed__ if version information isn't present. > **NB:** Dependency has been **updated** if both old and new version information is present. > **NB:** Dependency has been **added** if just the new version information is present. > **NB:** Dependency has been **removed** if version information isn't present.
assets/multiqc_config.yaml +2 −2 Original line number Diff line number Diff line Loading @@ -37,11 +37,11 @@ module_order: - bowtie2: name: 'Bowtie2 (target)' path_filters: - "./bowtie2/*target.bowtie2.log" - "./bowtie2/*.bowtie2.log" - bowtie2: name: 'Bowtie2 (spike-in)' path_filters: - "./bowtie2/*spikein.bowtie2.log" - "./bowtie2_spikein/*.bowtie2.log" - samtools - picard - custom_content Loading
bin/lib/reports.py +10 −4 Original line number Diff line number Diff line Loading @@ -99,10 +99,15 @@ class Reports: self.metadata_noctrl_table = pd.read_csv(self.meta_path, sep=',') self.metadata_table = pd.read_csv(self.meta_ctrl_path, sep=',') self.duplicate_info = False if 'dedup_percent_duplication' in self.metadata_table.columns: self.duplicate_info = True self.scale_factor_info = False if 'scale_factor' in self.metadata_table.columns: self.scale_factor_info = True # Make new perctenage alignment columns self.metadata_table['target_alignment_rate'] = self.metadata_table.loc[:, ('bt2_total_aligned_target')] / self.metadata_table.loc[:, ('bt2_total_reads_target')] * 100 self.metadata_table['spikein_alignment_rate'] = self.metadata_table.loc[:, ('bt2_total_aligned_spikein')] / self.metadata_table.loc[:, ('bt2_total_reads_spikein')] * 100 Loading Loading @@ -303,6 +308,7 @@ class Reports: data["04_replicate_heatmap"] = data5 # Plot section 6 if self.scale_factor_info == True: multi_plot, data6 = self.scale_factor_summary() plots["05_01_scale_factor"] = multi_plot[0] plots["05_02_frag_count"] = multi_plot[1] Loading
conf/base.config +3 −3 Original line number Diff line number Diff line Loading @@ -45,7 +45,7 @@ process { errorStrategy = 'retry' maxRetries = 2 } withName:CUSTOM_DUMPSOFTWAREVERSIONS { cache = false } // withName:CUSTOM_DUMPSOFTWAREVERSIONS { // cache = false // } }
