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Hello! This is an automated update of the following workflow: workflows/epigenetics/chipseq-sr. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.
By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0
The workflow release number has been updated from 0.12 to 0.13.
If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.
Output with path /tmp/tmpudjygeq4/MultiQC on data 19, data 10, and data 6 Stats__fe985593-2195-49e0-bfc4-73d404b1c7c8 different than expected
Expected line 'Sample MACS2_mqc_generalstats_macs2_d MACS2_mqc_generalstats_macs2_treatment_redundant_rate MACS2_mqc_generalstats_macs2_peak_count Bowtie 2 / HiSAT2_mqc_generalstats_bowtie_2_hisat2_overall_alignment_rate Cutadapt_mqc_generalstats_cutadapt_percent_trimmed' in output ('Sample macs2-d macs2-treatment_redundant_rate macs2-peak_count bowtie_2_hisat2-overall_alignment_rate cutadapt-percent_trimmed
wt_H3K4me3 200.0 0.0 4 98.37 4.612745098039215
')
die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/cutadapt_0 && ln -s '/tmp/tmpri2fp4q5/files/4/b/9/dataset_4b9550b6-31f5-4c87-91cf-f2dcbee3c3ff.dat' 'multiqc_WDir/cutadapt_0/wt_H3K4me3.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/wt_H3K4me3.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/wt_H3K4me3.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && mkdir multiqc_WDir/bowtie2_1 && grep -q '% overall alignment rate' /tmp/tmpri2fp4q5/files/a/3/8/dataset_a3860307-f1ff-4a4a-8e93-3c4419897a1e.dat || die "Module 'bowtie2: '% overall alignment rate' not found in the file 'wt_H3K4me3'" && ln -s '/tmp/tmpri2fp4q5/files/a/3/8/dataset_a3860307-f1ff-4a4a-8e93-3c4419897a1e.dat' 'multiqc_WDir/bowtie2_1/wt_H3K4me3' && mkdir multiqc_WDir/macs2_2 && grep -q "# This file is generated by MACS" /tmp/tmpri2fp4q5/files/0/4/c/dataset_04c2fae7-8829-4838-be95-73146c854d03.dat || die "'# This file is generated by MACS' not found in the file" && ln -s '/tmp/tmpri2fp4q5/files/0/4/c/dataset_04c2fae7-8829-4838-be95-73146c854d03.dat' 'multiqc_WDir/macs2_2/wt_H3K4me3_peaks.xls' && multiqc multiqc_WDir --filename 'report' --export && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true
Exit Code:
0
Standard Error:
/// MultiQC 🔍 v1.27 file_search | Search path: /tmp/tmpri2fp4q5/job_working_directory/000/8/working/multiqc_WDir macs2 | Found 1 logs bowtie2 | Found 1 reports cutadapt | Found 1 reports write_results | Rendering plots. Export plots to formats png, svg, pdf is requested, so it might take a while. To disable plot export, set `export_plots: false` in config, or remove the `--export-plots` command line flag write_results | Data : report_data write_results | Report : report.html write_results | Plots : report_plots multiqc | MultiQC complete
Standard Output:
total 124-rw-r--r-- 1 1001 118 88 Jan 27 05:06 bowtie2_se_plot.txt-rw-r--r-- 1 1001 118 80 Jan 27 05:06 cutadapt_filtered_reads_plot.txt-rw-r--r-- 1 1001 118 265 Jan 27 05:06 cutadapt_trimmed_sequences_plot_3_Counts.txt-rw-r--r-- 1 1001 118 350 Jan 27 05:06 cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt-rw-r--r-- 1 1001 118 769 Jan 27 05:06 multiqc.log-rw-r--r-- 1 1001 118 167 Jan 27 05:06 multiqc_bowtie2.txt-rw-r--r-- 1 1001 118 425 Jan 27 05:06 multiqc_citations.txt-rw-r--r-- 1 1001 118 206 Jan 27 05:06 multiqc_cutadapt.txt-rw-r--r-- 1 1001 118 77657 Jan 27 05:06 multiqc_data.json-rw-r--r-- 1 1001 118 174 Jan 27 05:06 multiqc_general_stats.txt-rw-r--r-- 1 1001 118 194 Jan 27 05:06 multiqc_macs.txt-rw-r--r-- 1 1001 118 51 Jan 27 05:06 multiqc_software_versions.txt-rw-r--r-- 1 1001 118 417 Jan 27 05:06 multiqc_sources.txt
INFO @ Mon, 27 Jan 2025 05:05:50:
# Command line: callpeak -t /tmp/tmpri2fp4q5/files/7/5/b/dataset_75b116d9-ea96-48b9-abd7-2bd2eabbc6ac.dat --name wt_H3K4me3 --format BAM --gsize 1870000000 --SPMR --call-summits --keep-dup 1 --d-min 20 --buffer-size 100000 --bdg --qvalue 0.05 --nomodel --extsize 200 --shift 0
# ARGUMENTS LIST:
# name = wt_H3K4me3
# format = BAM
# ChIP-seq file = ['/tmp/tmpri2fp4q5/files/7/5/b/dataset_75b116d9-ea96-48b9-abd7-2bd2eabbc6ac.dat']
# control file = None
# effective genome size = 1.87e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Paired-End mode is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million readsINFO @ Mon, 27 Jan 2025 05:05:50: #1 read tag files... INFO @ Mon, 27 Jan 2025 05:05:50: #1 read treatment tags... INFO @ Mon, 27 Jan 2025 05:05:50: 44078 reads have been read. INFO @ Mon, 27 Jan 2025 05:05:50: #1 tag size is determined as 49 bps INFO @ Mon, 27 Jan 2025 05:05:50: #1 tag size = 49.0 INFO @ Mon, 27 Jan 2025 05:05:50: #1 total tags in treatment: 44078 INFO @ Mon, 27 Jan 2025 05:05:50: #1 user defined the maximum tags... INFO @ Mon, 27 Jan 2025 05:05:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 27 Jan 2025 05:05:50: #1 tags after filtering in treatment: 44038 INFO @ Mon, 27 Jan 2025 05:05:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 27 Jan 2025 05:05:50: #1 finished! INFO @ Mon, 27 Jan 2025 05:05:50: #2 Build Peak Model... INFO @ Mon, 27 Jan 2025 05:05:50: #2 Skipped... INFO @ Mon, 27 Jan 2025 05:05:50: #2 Use 200 as fragment length INFO @ Mon, 27 Jan 2025 05:05:50: #3 Call peaks... INFO @ Mon, 27 Jan 2025 05:05:50: #3 Going to call summits inside each peak ... INFO @ Mon, 27 Jan 2025 05:05:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 27 Jan 2025 05:05:50: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 27 Jan 2025 05:05:50: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... wt_H3K4me3_treat_pileup.bdg INFO @ Mon, 27 Jan 2025 05:05:50: #3 Write bedGraph files for control lambda (after scaling if necessary)... wt_H3K4me3_control_lambda.bdg INFO @ Mon, 27 Jan 2025 05:05:50: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ Mon, 27 Jan 2025 05:05:50: #3 Call peaks for each chromosome... INFO @ Mon, 27 Jan 2025 05:05:51: #4 Write output xls file... wt_H3K4me3_peaks.xls INFO @ Mon, 27 Jan 2025 05:05:51: #4 Write peak in narrowPeak format file... wt_H3K4me3_peaks.narrowPeak INFO @ Mon, 27 Jan 2025 05:05:51: #4 Write summits bed file... wt_H3K4me3_summits.bed INFO @ Mon, 27 Jan 2025 05:05:51: Done!
Output with path /tmp/tmpok8sf15n/MultiQC on data 19, data 10, and data 6 Stats__9d92ddad-2832-465f-8120-9c524820af14 different than expected
Expected line 'Sample macs2-d macs2-d macs2-treatment_redundant_rate macs2-peak_count bowtie_2_hisat2-overall_alignment_rate cutadapt-percent_trimmed' in output ('Sample macs2-d macs2-treatment_redundant_rate macs2-peak_count bowtie_2_hisat2-overall_alignment_rate cutadapt-percent_trimmed
wt_H3K4me3 200.0 0.0 4 98.37 4.612745098039215
')
die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/cutadapt_0 && ln -s '/tmp/tmpxpuy967v/files/a/d/8/dataset_ad8ca5d4-a6c3-4b8f-adff-d748a78f068f.dat' 'multiqc_WDir/cutadapt_0/wt_H3K4me3.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/wt_H3K4me3.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/wt_H3K4me3.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && mkdir multiqc_WDir/bowtie2_1 && grep -q '% overall alignment rate' /tmp/tmpxpuy967v/files/b/4/e/dataset_b4e82b94-b091-42ef-b711-45297504a2ac.dat || die "Module 'bowtie2: '% overall alignment rate' not found in the file 'wt_H3K4me3'" && ln -s '/tmp/tmpxpuy967v/files/b/4/e/dataset_b4e82b94-b091-42ef-b711-45297504a2ac.dat' 'multiqc_WDir/bowtie2_1/wt_H3K4me3' && mkdir multiqc_WDir/macs2_2 && grep -q "# This file is generated by MACS" /tmp/tmpxpuy967v/files/d/9/3/dataset_d9309b89-15b3-4e10-9b9d-7fb251b935b7.dat || die "'# This file is generated by MACS' not found in the file" && ln -s '/tmp/tmpxpuy967v/files/d/9/3/dataset_d9309b89-15b3-4e10-9b9d-7fb251b935b7.dat' 'multiqc_WDir/macs2_2/wt_H3K4me3_peaks.xls' && multiqc multiqc_WDir --filename 'report' --export && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true
Exit Code:
0
Standard Error:
/// MultiQC 🔍 v1.27 file_search | Search path: /tmp/tmpxpuy967v/job_working_directory/000/8/working/multiqc_WDir macs2 | Found 1 logs bowtie2 | Found 1 reports cutadapt | Found 1 reports write_results | Rendering plots. Export plots to formats png, svg, pdf is requested, so it might take a while. To disable plot export, set `export_plots: false` in config, or remove the `--export-plots` command line flag write_results | Data : report_data write_results | Report : report.html write_results | Plots : report_plots multiqc | MultiQC complete
Standard Output:
total 124-rw-r--r-- 1 1001 118 88 Jan 29 13:58 bowtie2_se_plot.txt-rw-r--r-- 1 1001 118 80 Jan 29 13:58 cutadapt_filtered_reads_plot.txt-rw-r--r-- 1 1001 118 265 Jan 29 13:58 cutadapt_trimmed_sequences_plot_3_Counts.txt-rw-r--r-- 1 1001 118 350 Jan 29 13:58 cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt-rw-r--r-- 1 1001 118 769 Jan 29 13:58 multiqc.log-rw-r--r-- 1 1001 118 167 Jan 29 13:58 multiqc_bowtie2.txt-rw-r--r-- 1 1001 118 425 Jan 29 13:58 multiqc_citations.txt-rw-r--r-- 1 1001 118 206 Jan 29 13:58 multiqc_cutadapt.txt-rw-r--r-- 1 1001 118 77657 Jan 29 13:58 multiqc_data.json-rw-r--r-- 1 1001 118 174 Jan 29 13:58 multiqc_general_stats.txt-rw-r--r-- 1 1001 118 194 Jan 29 13:58 multiqc_macs.txt-rw-r--r-- 1 1001 118 51 Jan 29 13:58 multiqc_software_versions.txt-rw-r--r-- 1 1001 118 417 Jan 29 13:58 multiqc_sources.txt
INFO @ Wed, 29 Jan 2025 13:57:30:
# Command line: callpeak -t /tmp/tmpxpuy967v/files/0/b/e/dataset_0be82f4c-f124-4639-a2bb-70658fd6df7e.dat --name wt_H3K4me3 --format BAM --gsize 1870000000 --SPMR --call-summits --keep-dup 1 --d-min 20 --buffer-size 100000 --bdg --qvalue 0.05 --nomodel --extsize 200 --shift 0
# ARGUMENTS LIST:
# name = wt_H3K4me3
# format = BAM
# ChIP-seq file = ['/tmp/tmpxpuy967v/files/0/b/e/dataset_0be82f4c-f124-4639-a2bb-70658fd6df7e.dat']
# control file = None
# effective genome size = 1.87e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Paired-End mode is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million readsINFO @ Wed, 29 Jan 2025 13:57:30: #1 read tag files... INFO @ Wed, 29 Jan 2025 13:57:30: #1 read treatment tags... INFO @ Wed, 29 Jan 2025 13:57:30: 44078 reads have been read. INFO @ Wed, 29 Jan 2025 13:57:30: #1 tag size is determined as 49 bps INFO @ Wed, 29 Jan 2025 13:57:30: #1 tag size = 49.0 INFO @ Wed, 29 Jan 2025 13:57:30: #1 total tags in treatment: 44078 INFO @ Wed, 29 Jan 2025 13:57:30: #1 user defined the maximum tags... INFO @ Wed, 29 Jan 2025 13:57:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 29 Jan 2025 13:57:30: #1 tags after filtering in treatment: 44038 INFO @ Wed, 29 Jan 2025 13:57:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 29 Jan 2025 13:57:30: #1 finished! INFO @ Wed, 29 Jan 2025 13:57:30: #2 Build Peak Model... INFO @ Wed, 29 Jan 2025 13:57:30: #2 Skipped... INFO @ Wed, 29 Jan 2025 13:57:30: #2 Use 200 as fragment length INFO @ Wed, 29 Jan 2025 13:57:30: #3 Call peaks... INFO @ Wed, 29 Jan 2025 13:57:30: #3 Going to call summits inside each peak ... INFO @ Wed, 29 Jan 2025 13:57:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 29 Jan 2025 13:57:30: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Wed, 29 Jan 2025 13:57:30: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... wt_H3K4me3_treat_pileup.bdg INFO @ Wed, 29 Jan 2025 13:57:30: #3 Write bedGraph files for control lambda (after scaling if necessary)... wt_H3K4me3_control_lambda.bdg INFO @ Wed, 29 Jan 2025 13:57:30: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ Wed, 29 Jan 2025 13:57:30: #3 Call peaks for each chromosome... INFO @ Wed, 29 Jan 2025 13:57:30: #4 Write output xls file... wt_H3K4me3_peaks.xls INFO @ Wed, 29 Jan 2025 13:57:30: #4 Write peak in narrowPeak format file... wt_H3K4me3_peaks.narrowPeak INFO @ Wed, 29 Jan 2025 13:57:30: #4 Write summits bed file... wt_H3K4me3_summits.bed INFO @ Wed, 29 Jan 2025 13:57:30: Done!
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Hello! This is an automated update of the following workflow: workflows/epigenetics/chipseq-sr. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.
By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0should be updated totoolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0The workflow release number has been updated from 0.12 to 0.13.
If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.