chipseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues2019-05-16T09:10:45-05:00https://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 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/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/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/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/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/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/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/44diffbind design file error2020-06-23T15:51:25-05:00Spencer Barnesdiffbind design file errorThe step that creates the diffbind design file copies the SampleID column into the Condition column. This causes an error since this causes diffbind to compare N different conditions instead of the expected 2 or 3. Possible fix would cha...The step that creates the diffbind design file copies the SampleID column into the Condition column. This causes an error since this causes diffbind to compare N different conditions instead of the expected 2 or 3. Possible fix would change the diffbind script to compare Factor or Treatment as default.2.0.0Spencer BarnesSpencer Barneshttps://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/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/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/chipseq_analysis/-/issues/40Astrocyte wrong design file2019-05-06T14:19:08-05:00Venkat MalladiAstrocyte wrong design fileVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/39Optimizations2020-06-23T15:51:07-05:00Jonathan GesellOptimizationsGeneral speed-ups and optimization of pipeline branches.General speed-ups and optimization of pipeline branches.3.0.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/38Missing modules2019-04-23T07:48:40-05:00Venkat MalladiMissing modules1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/37Fix software versions test2019-04-22T22:30:59-05:00Venkat MalladiFix software versions test1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/36Update Astrocyte documentation and errors2019-04-22T22:18:14-05:00Venkat MalladiUpdate Astrocyte documentation and errors1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/35Fix astrocyte run2019-04-22T15:17:51-05:00Venkat MalladiFix astrocyte runAstrocyte is not using the correct variables in Main.nfAstrocyte is not using the correct variables in Main.nf1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/34Fix tests for software versions2019-04-20T03:12:15-05:00Venkat MalladiFix tests for software versions1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/33New folders for all steps2019-03-16T19:26:26-05:00Venkat MalladiNew folders for all stepsBreak steps into sub-folders by Sample, or Experiment where appropriateBreak steps into sub-folders by Sample, or Experiment where appropriate1.0.0Venkat MalladiVenkat Malladi