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commented
3 months ago Test Results (powered by Planemo)
Test Summary
| Test State | Count |
|---|---|
| Total | 1 |
| Passed | 0 |
| Error | 0 |
| Failure | 1 |
| Skipped | 0 |
Failed Tests
*❌ chipseq-pe.ga_0
**Problems**:
* ```
Output with path /tmp/tmpmwr242_q/cutadapt__00e53866-ff8b-4ecb-bd35-f96151aa6b0a different than expected
Expected text '4.8 50000 587 550 3693 46307 5100000' in output ('Sample cutadapt_version pairs_processed r1_with_adapters r2_with_adapters pairs_too_short pairs_written bp_processed quality_trimmed bp_written percent_trimmed
wt_H3K4me3_2 4.9 50000 587 550 3693 46307 5100000 367032 4573330 10.326862745098039
')
```
#### Workflow invocation details
* Invocation Messages
*
Steps
- **Step 1: PE fastq input**: * step_state: scheduled - **Step 2: adapter_forward**: * step_state: scheduled - **Step 11: summary of MACS2**: * step_state: scheduled *Jobs
- **Job 1:** * Job state is ok **Command Line:** * ```console grep -P -A 0 -B 0 --no-group-separator -i -- '^#' '/tmp/tmp34hd7jyi/files/b/8/8/dataset_b88b25a4-b76f-4417-9d91-afffcbb70596.dat' > '/tmp/tmp34hd7jyi/job_working_directory/000/7/outputs/dataset_987ece69-8723-4e86-9272-9827409eb2c3.dat' ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "bf546648426411efa0f215ccd09124e3" ` | | case\_sensitive | ` "-i" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len" ` | | color | ` "NOCOLOR" ` | | dbkey | ` "mm10" ` | | invert | ` "" ` | | lines\_after | ` "0" ` | | lines\_before | ` "0" ` | | regex\_type | ` "-P" ` | | url\_paste | ` "^#" ` | - **Step 12: Bigwig from MACS2**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
grep -v "^track" '/tmp/tmp34hd7jyi/files/0/1/e/dataset_01e7da65-178a-4546-a6c2-5109b7619d74.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len' '/tmp/tmp34hd7jyi/job_working_directory/000/8/outputs/dataset_ee5e2f15-91fd-4079-aa4a-0df210d9090a.dat' -clip 2>&1 || echo "Error running wigToBigWig." >&2
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "bedgraph" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "bf546648426411efa0f215ccd09124e3" ` |
| chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len" ` |
| dbkey | ` "mm10" ` |
| settings | ` {"__current_case__": 0, "settingsType": "preset"} ` |
</details>
- **Step 13: MultiQC**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/cutadapt_0 && ln -s '/tmp/tmp34hd7jyi/files/b/d/6/dataset_bd67135c-cb9e-4ebf-934f-db5cc6a49d7e.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/tmp34hd7jyi/files/5/e/1/dataset_5e12ac61-2216-47d5-af0f-830ca856a547.dat || die "Module 'bowtie2: '% overall alignment rate' not found in the file 'wt_H3K4me3'" && ln -s '/tmp/tmp34hd7jyi/files/5/e/1/dataset_5e12ac61-2216-47d5-af0f-830ca856a547.dat' 'multiqc_WDir/bowtie2_1/wt_H3K4me3' && mkdir multiqc_WDir/macs2_2 && grep -q "# This file is generated by MACS" /tmp/tmp34hd7jyi/files/b/8/8/dataset_b88b25a4-b76f-4417-9d91-afffcbb70596.dat || die "'# This file is generated by MACS' not found in the file" && ln -s '/tmp/tmp34hd7jyi/files/b/8/8/dataset_b88b25a4-b76f-4417-9d91-afffcbb70596.dat' 'multiqc_WDir/macs2_2/wt_H3K4me3_peaks.xls' && multiqc multiqc_WDir --filename 'report' --export
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/// MultiQC 🔍 | v1.11
| multiqc | MultiQC Version v1.23 now available!
| multiqc | Search path : /tmp/tmp34hd7jyi/job_working_directory/000/9/working/multiqc_WDir
| macs2 | Found 1 logs
| bowtie2 | Found 1 reports
| cutadapt | Found 1 reports
| multiqc | Compressing plot data
| multiqc | Report : report.html
| multiqc | Data : report_data
| multiqc | Plots : report_plots
| multiqc | MultiQC complete
```
**Standard Output:**
* ```console
| searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "bf546648426411efa0f215ccd09124e3" ` |
| chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len" ` |
| comment | ` "" ` |
| dbkey | ` "mm10" ` |
| export | ` true ` |
| flat | ` false ` |
| results | ` [{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}, {"__index__": 1, "software_cond": {"__current_case__": 3, "input": {"values": [{"id": 5, "src": "hdca"}]}, "software": "bowtie2"}}, {"__index__": 2, "software_cond": {"__current_case__": 16, "input": {"values": [{"id": 7, "src": "hdca"}]}, "software": "macs2"}}] ` |
| saveLog | ` false ` |
| title | ` "" ` |
</details>
- **Step 3: adapter_reverse**:
* step_state: scheduled
- **Step 4: reference_genome**:
* step_state: scheduled
- **Step 5: effective_genome_size**:
* step_state: scheduled
- **Step 6: normalize_profile**:
* step_state: scheduled
- **Step 7: Cutadapt (remove adapter + bad quality bases)**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -f -s '/tmp/tmp34hd7jyi/files/0/9/8/dataset_098744ef-67b0-4e6d-9536-5cc59e714d80.dat' 'wt_H3K4me3_1.fq' && ln -f -s '/tmp/tmp34hd7jyi/files/5/f/8/dataset_5f8b917e-6997-458f-b2ff-1582ead2dfaa.dat' 'wt_H3K4me3_2.fq' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC '='GATCGGAAGAGCACACGTCTGAACTCCAGTCAC' -A 'Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'='GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT' --error-rate=0.1 --times=1 --overlap=3 --action=trim --quality-cutoff=30 --minimum-length=15 -o 'out1.fq' -p 'out2.fq' 'wt_H3K4me3_1.fq' 'wt_H3K4me3_2.fq' > report.txt
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "bf546648426411efa0f215ccd09124e3" ` |
| adapter\_options | ` {"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"} ` |
| chromInfo | ` "/tmp/tmp34hd7jyi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| filter\_options | ` {"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "15", "minimum_length2": null, "pair_filter": "any"} ` |
| library | ` {"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "GATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "adapter_name": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC ", "adapter_source_list": "user"}, "single_noindels": false}], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", "adapter_name": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", "adapter_source_list": "user"}, "single_noindels": false}], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"} ` |
| other\_trimming\_options | ` {"cut": "0", "cut2": "0", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "30", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false} ` |
| output\_selector | ` ["report"] ` |
| read\_mod\_options | ` {"length_tag": "", "rename": "", "strip_suffix": "", "zero_cap": false} ` |
</details>
- **Step 8: Bowtie2 map on reference**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
set -o | grep -q pipefail && set -o pipefail; ln -f -s '/tmp/tmp34hd7jyi/files/f/1/8/dataset_f18070c3-5014-4ac1-9e13-52faf6c6e782.dat' input_f.fastq && ln -f -s '/tmp/tmp34hd7jyi/files/7/1/2/dataset_712802b9-deaa-4813-9c47-fee96cc1b924.dat' input_r.fastq && THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi && bowtie2 -p "$THREADS" -x '/cvmfs/data.galaxyproject.org/byhand/mm10/bowtie2_index/mm10' -1 'input_f.fastq' -2 'input_r.fastq' 2> >(tee '/tmp/tmp34hd7jyi/job_working_directory/000/4/outputs/dataset_5e12ac61-2216-47d5-af0f-830ca856a547.dat' >&2) | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmp34hd7jyi/job_working_directory/000/4/outputs/dataset_6f1753df-9b19-46c6-83f3-61623aa4d2a0.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
46307 reads; of these:
46307 (100.00%) were paired; of these:
1292 (2.79%) aligned concordantly 0 times
39329 (84.93%) aligned concordantly exactly 1 time
5686 (12.28%) aligned concordantly >1 times
----
1292 pairs aligned concordantly 0 times; of these:
259 (20.05%) aligned discordantly 1 time
----
1033 pairs aligned 0 times concordantly or discordantly; of these:
2066 mates make up the pairs; of these:
1220 (59.05%) aligned 0 times
506 (24.49%) aligned exactly 1 time
340 (16.46%) aligned >1 times
98.68% overall alignment rate
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "bf546648426411efa0f215ccd09124e3" ` |
| analysis\_type | ` {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"} ` |
| chromInfo | ` "/tmp/tmp34hd7jyi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| library | ` {"__current_case__": 2, "aligned_file": false, "input_1": {"values": [{"id": 4, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false} ` |
| reference\_genome | ` {"__current_case__": 0, "index": "mm10", "source": "indexed"} ` |
| rg | ` {"__current_case__": 3, "rg_selector": "do_not_set"} ` |
| sam\_options | ` {"__current_case__": 1, "sam_options_selector": "no"} ` |
| save\_mapping\_stats | ` true ` |
</details>
- **Step 9: filter MAPQ30 concordent pairs**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -s '/tmp/tmp34hd7jyi/files/6/f/1/dataset_6f1753df-9b19-46c6-83f3-61623aa4d2a0.dat' input.bam && ln -s '/tmp/tmp34hd7jyi/files/_metadata_files/2/6/2/metadata_262b3531-d923-4f77-a827-33d166c62947.dat' input.bai && samtools view -o '/tmp/tmp34hd7jyi/job_working_directory/000/5/outputs/dataset_d4afc944-1e3c-4e76-a1de-a68fa22fbd21.dat' -h -b -q 30 -f 0x2 input.bam
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "bam" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "bf546648426411efa0f215ccd09124e3" ` |
| bed\_file | ` None ` |
| chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len" ` |
| dbkey | ` "mm10" ` |
| flag | ` {"__current_case__": 1, "filter": "yes", "reqBits": ["0x0002"], "skipBits": null} ` |
| header | ` "-h" ` |
| library | ` "" ` |
| mapq | ` "30" ` |
| outputtype | ` "bam" ` |
| possibly\_select\_inverse | ` false ` |
| read\_group | ` "" ` |
| regions | ` "" ` |
</details>
- **Step 10: Call Peaks with MACS2**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
export PYTHON_EGG_CACHE=`pwd` && (macs2 callpeak -t '/tmp/tmp34hd7jyi/files/d/4/a/dataset_d4afc944-1e3c-4e76-a1de-a68fa22fbd21.dat' --name wt_H3K4me3 --format BAMPE --gsize '1870000000' --SPMR --call-summits --keep-dup '1' --d-min 20 --buffer-size 100000 --bdg --qvalue '0.05' --mfold '5' '50' --bw '300' 2>&1 > macs2_stderr) && cp wt_H3K4me3_peaks.xls '/tmp/tmp34hd7jyi/job_working_directory/000/6/outputs/dataset_b88b25a4-b76f-4417-9d91-afffcbb70596.dat' && ( count=`ls -1 wt_H3K4me3* 2>/dev/null | wc -l`; if [ $count != 0 ]; then mkdir '/tmp/tmp34hd7jyi/job_working_directory/000/6/outputs/dataset_f9aff3f3-c486-44e7-945a-505e68276e85_files' && cp -r wt_H3K4me3* '/tmp/tmp34hd7jyi/job_working_directory/000/6/outputs/dataset_f9aff3f3-c486-44e7-945a-505e68276e85_files' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/macs2/86e2413cf3f8/macs2/dir2html.py' '/tmp/tmp34hd7jyi/job_working_directory/000/6/outputs/dataset_f9aff3f3-c486-44e7-945a-505e68276e85_files' macs2_stderr > '/tmp/tmp34hd7jyi/job_working_directory/000/6/outputs/dataset_f9aff3f3-c486-44e7-945a-505e68276e85.dat'; fi; ) && exit_code_for_galaxy=$? && cat macs2_stderr 2>&1 && (exit $exit_code_for_galaxy)
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
INFO @ Mon, 15 Jul 2024 04:47:49:
# Command line: callpeak -t /tmp/tmp34hd7jyi/files/d/4/a/dataset_d4afc944-1e3c-4e76-a1de-a68fa22fbd21.dat --name wt_H3K4me3 --format BAMPE --gsize 1870000000 --SPMR --call-summits --keep-dup 1 --d-min 20 --buffer-size 100000 --bdg --qvalue 0.05 --mfold 5 50 --bw 300
# ARGUMENTS LIST:
# name = wt_H3K4me3
# format = BAMPE
# ChIP-seq file = ['/tmp/tmp34hd7jyi/files/d/4/a/dataset_d4afc944-1e3c-4e76-a1de-a68fa22fbd21.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 on
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
INFO @ Mon, 15 Jul 2024 04:47:49: #1 read fragment files...
INFO @ Mon, 15 Jul 2024 04:47:49: #1 read treatment fragments...
INFO @ Mon, 15 Jul 2024 04:47:49: 41724 fragments have been read.
INFO @ Mon, 15 Jul 2024 04:47:49: #1 mean fragment size is determined as 201.8 bp from treatment
INFO @ Mon, 15 Jul 2024 04:47:49: #1 fragment size = 201.8
INFO @ Mon, 15 Jul 2024 04:47:49: #1 total fragments in treatment: 41724
INFO @ Mon, 15 Jul 2024 04:47:49: #1 user defined the maximum fragments...
INFO @ Mon, 15 Jul 2024 04:47:49: #1 filter out redundant fragments by allowing at most 1 identical fragment(s)
INFO @ Mon, 15 Jul 2024 04:47:49: #1 fragments after filtering in treatment: 41724
INFO @ Mon, 15 Jul 2024 04:47:49: #1 Redundant rate of treatment: 0.00
INFO @ Mon, 15 Jul 2024 04:47:49: #1 finished!
INFO @ Mon, 15 Jul 2024 04:47:49: #2 Build Peak Model...
INFO @ Mon, 15 Jul 2024 04:47:49: #2 Skipped...
INFO @ Mon, 15 Jul 2024 04:47:49: #3 Call peaks...
INFO @ Mon, 15 Jul 2024 04:47:49: #3 Going to call summits inside each peak ...
INFO @ Mon, 15 Jul 2024 04:47:49: #3 Pre-compute pvalue-qvalue table...
INFO @ Mon, 15 Jul 2024 04:47:49: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Mon, 15 Jul 2024 04:47:49: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... wt_H3K4me3_treat_pileup.bdg
INFO @ Mon, 15 Jul 2024 04:47:49: #3 Write bedGraph files for control lambda (after scaling if necessary)... wt_H3K4me3_control_lambda.bdg
INFO @ Mon, 15 Jul 2024 04:47:49: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Mon, 15 Jul 2024 04:47:49: #3 Call peaks for each chromosome...
INFO @ Mon, 15 Jul 2024 04:47:49: #4 Write output xls file... wt_H3K4me3_peaks.xls
INFO @ Mon, 15 Jul 2024 04:47:49: #4 Write peak in narrowPeak format file... wt_H3K4me3_peaks.narrowPeak
INFO @ Mon, 15 Jul 2024 04:47:49: #4 Write summits bed file... wt_H3K4me3_summits.bed
INFO @ Mon, 15 Jul 2024 04:47:49: Done!
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "bf546648426411efa0f215ccd09124e3" ` |
| advanced\_options | ` {"broad_options": {"__current_case__": 1, "broad_options_selector": "nobroad", "call_summits": true}, "buffer_size": "100000", "d_min": "20", "keep_dup_options": {"__current_case__": 1, "keep_dup_options_selector": "1"}, "llocal": null, "nolambda": false, "ratio": null, "slocal": null, "spmr": true, "to_large": false} ` |
| chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len" ` |
| control | ` {"__current_case__": 1, "c_select": "No"} ` |
| cutoff\_options | ` {"__current_case__": 1, "cutoff_options_selector": "qvalue", "qvalue": "0.05"} ` |
| dbkey | ` "mm10" ` |
| effective\_genome\_size\_options | ` {"__current_case__": 4, "effective_genome_size_options_selector": "user_defined", "gsize": "1870000000"} ` |
| format | ` "BAMPE" ` |
| nomodel\_type | ` {"__current_case__": 0, "band_width": "300", "mfold_lower": "5", "mfold_upper": "50", "nomodel_type_selector": "create_model"} ` |
| outputs | ` ["peaks_tabular", "summits", "bdg", "html"] ` |
| treatment | ` {"__current_case__": 0, "input_treatment_file": {"values": [{"id": 10, "src": "dce"}]}, "t_multi_select": "No"} ` |
</details>
</details>-
Other invocation details
- **history_id** * a8bf451482af11ab - **history_state** * ok - **invocation_id** * a8bf451482af11ab - **invocation_state** * scheduled - **workflow_id** * a8bf451482af11ab
Hello! This is an automated update of the following workflow: workflows/epigenetics/chipseq-pe. 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/lparsons/cutadapt/cutadapt/4.8+galaxy1should be updated totoolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0The workflow release number has been updated from 0.10 to 0.11.