BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-04-26T18:34:24-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/45Multiqc failure2020-04-26T18:34:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMultiqc failure# Summary
MultiQC step fail when submitted CLI for some users
# Steps to reproduce
`nextflow run` by user with matplotlib > 3.1.2 installed
# Observed bug behavior
python error
# Expected behavior
pass
# Relevant logs and/or screensh...# Summary
MultiQC step fail when submitted CLI for some users
# Steps to reproduce
`nextflow run` by user with matplotlib > 3.1.2 installed
# Observed bug behavior
python error
# Expected behavior
pass
# Relevant logs and/or screenshots
```
pkg_resources.VersionConflict: (matplotlib 3.2.1 (/home2/ghenry/.local/lib/python3.6/site-packages), Requirement.parse('matplotlib<3.1.2,>=2.1.1'))
```
# Potential fixes
Remove depreciated module command in multiqc process (pipeline uses docker container now and does not require modules)
/cc @ghenryhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/41Add test for astrocyte specific run of pipline2020-10-30T11:48:42-05:00Venkat MalladiAdd test for astrocyte specific run of pipline# Summary
* [x] Add test for astrocyte-specific test besides cli
* [x] Add Badge for astrocyte
* [x] Test for astrocyte 0.4.0 instead of loading astrocyte
/cc @ghenry @venkat.malladi @s181706 @s189701# Summary
* [x] Add test for astrocyte-specific test besides cli
* [x] Add Badge for astrocyte
* [x] Test for astrocyte 0.4.0 instead of loading astrocyte
/cc @ghenry @venkat.malladi @s181706 @s189701https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/41DesignFile path not followed2019-05-06T15:31:23-05:00Venkat MalladiDesignFile path not followedUpdate main.nf to have design file followed.Update main.nf to have design file followed.Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/41Update multiqc version/references report2020-07-01T14:36:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)Version 2.1.0https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/46Add simple integration CI test2020-11-03T12:29:40-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd simple integration CI testto branches except master and develop to test nextflow run on branchesto branches except master and develop to test nextflow run on branches3.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/42Update to Astocyte 0.4.02020-09-07T06:43:20-05:00Venkat MalladiUpdate to Astocyte 0.4.0# Summary
New Astrocyte 0.4.0 features to test
* [x] Customized configuration file in yaml
* [x] Load specific singularity version
* [x] Load Nextflow version
* [x] Add citation in yaml file
/cc @ghenry @venkat.malladi @s18170...# Summary
New Astrocyte 0.4.0 features to test
* [x] Customized configuration file in yaml
* [x] Load specific singularity version
* [x] Load Nextflow version
* [x] Add citation in yaml file
/cc @ghenry @venkat.malladi @s181706 @s189701Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/42Retitle skipDiff and skipMotif2019-05-15T09:25:31-05:00Venkat MalladiRetitle skipDiff and skipMotifInput parameters include default values of `skipDiff` and `skipMotif` to `false` meaning those steps are run, but on astrocyte, input asks if you want to run those steps. If `true` is selected, then those steps are actually skipped.Input parameters include default values of `skipDiff` and `skipMotif` to `false` meaning those steps are run, but on astrocyte, input asks if you want to run those steps. If `true` is selected, then those steps are actually skipped.1.0.4Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/42Update to astrocyte 0.3.12020-07-01T14:35:53-05:00Venkat MalladiUpdate to astrocyte 0.3.1Version 2.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/10Add ability to count additional features2020-06-21T13:57:51-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd ability to count additional featureshttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customhttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customPendingGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/43failure to load python module-motif search2019-05-15T09:26:13-05:00Spencer Barnesfailure to load python module-motif searchMay-07 17:29:04.313 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'motifSearch (1)'Caused by:
Process `motifSearch (1)` terminated with an error exit status (1)Command executed: module load meme/4...May-07 17:29:04.313 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'motifSearch (1)'Caused by:
Process `motifSearch (1)` terminated with an error exit status (1)Command executed: module load meme/4.11.1-gcc-openmpi
module load bedtools/2.26.0
python3 /project/apps/astrocyte/data/runs/2200/2278/workflow/scripts/motif_search.py -d
design_annotatePeaks.tsv -g /project/shared/bicf_workflow_ref/GRCm38/genome.fa.txt -p
600Command exit status:
1Command output:
(empty)Command error:
Traceback (most recent call last):
File "/project/apps/astrocyte/data/runs/2200/2278/workflow/scripts/motif_search.py", line 11, in <module>
import pandas as pd
** ModuleNotFoundError: No module named 'pandas'**1.0.4Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/43map reads fails to make bam files for long reads2020-07-29T07:44:38-05:00Venkat Malladimap reads fails to make bam files for long readshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/blob/dev/workflow/scripts/map_reads.py#L239
Doesn't make sam files or bam fileshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/blob/dev/workflow/scripts/map_reads.py#L239
Doesn't make sam files or bam filesVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/52Generate QC Plot2020-09-18T12:33:29-05:00Jeremy MathewsGenerate QC PlotIn preparation for a Seurat analysis workflow, the addition of a Violin Plot to display QC for count results can be used to determine inputs for Seurat workflow.
@ghenry has an automated script to determine optimal cutoff values for fil...In preparation for a Seurat analysis workflow, the addition of a Violin Plot to display QC for count results can be used to determine inputs for Seurat workflow.
@ghenry has an automated script to determine optimal cutoff values for filtering data. Use the violin plot code below and overlay it with markers of cutoff values.
If values are acceptable, then use "automatic" option in Seurat workflow, else use "manual" and select the cutoffs for filtering data by hand.
"""
VlnPlot(object, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3)
"""https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/45Remove spaces and "weird characters" from design files2019-07-30T09:16:32-05:00Holly RuessRemove spaces and "weird characters" from design files[design.tsv](/uploads/97cb32a15d52c0d7efdff112e1adefd2/design.tsv)
See attached design file. Remove spaces after names and test for weird characters (. - _ ,) to see which programs fail and then remove those at the check design file[design.tsv](/uploads/97cb32a15d52c0d7efdff112e1adefd2/design.tsv)
See attached design file. Remove spaces after names and test for weird characters (. - _ ,) to see which programs fail and then remove those at the check design file1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/46Fix Astrocyte links2019-05-15T09:28:20-05:00Holly RuessFix Astrocyte linksLinks from git (for instance design files examples) are not working in AstrocyteLinks from git (for instance design files examples) are not working in Astrocyte1.0.4Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/47annotate peaks2020-03-20T23:12:11-05:00Holly Ruessannotate peaksuse gtf file for the annotate peaks step instead of libraries TxDb and orguse gtf file for the annotate peaks step instead of libraries TxDb and org1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/48Single control fails at pool_and_psuedoreplicate2019-05-15T09:29:54-05:00Holly RuessSingle control fails at pool_and_psuedoreplicateThe pool_and_psuedoreplicate needs an update to use a single control sample. The current code doesn't workThe pool_and_psuedoreplicate needs an update to use a single control sample. The current code doesn't work1.0.4Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/49check design file failure2019-05-14T15:18:14-05:00Spencer Barnescheck design file failureCurrently check design file step still fails if project is single-end but `fastq_read2` header is not present in design file.Currently check design file step still fails if project is single-end but `fastq_read2` header is not present in design file.1.1.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/50Change Tests for Peak comparison to be greater than or equal to2019-05-15T10:02:03-05:00Venkat MalladiChange Tests for Peak comparison to be greater than or equal to1.0.4Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/51Add in merge request template2019-05-15T13:19:11-05:00Venkat MalladiAdd in merge request templateVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/52Astrocyte Bug Fixes2019-05-16T09:10:45-05:00Venkat MalladiAstrocyte Bug Fixes- Fix generalized tests
- Links in astrocyte- Fix generalized tests
- Links in astrocyte1.0.4Venkat MalladiVenkat Malladi