BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-05-02T14:54:34-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/13An error in 'trimgalore.sh'2019-05-02T14:54:34-05:00Jeon LeeAn error in 'trimgalore.sh'Hi,
An user, skim17, reported an error generated during the 'trim' step such as [Process `trim (3)` terminated with an error exit status (1)]. After looking at the relevant scripts, we suspect that the error came from some lines in 'trim...Hi,
An user, skim17, reported an error generated during the 'trim' step such as [Process `trim (3)` terminated with an error exit status (1)]. After looking at the relevant scripts, we suspect that the error came from some lines in 'trimgalore.sh' below:
r1base="${fq1%.fastq*}"
r2base="${fq2%.fastq*}"
source /etc/profile.d/modules.sh
module load trimgalore/0.4.1 cutadapt/1.9.1
if [ -s $fq2 ]
then
trim_galore --paired -q 25 --illumina --gzip --length 35 ${fq1} ${fq2}
mv ${r1base}_val_1.fq.gz ${pair_id}.trim.R1.fastq.gz
mv ${r2base}_val_2.fq.gz ${pair_id}.trim.R2.fastq.gz
else
trim_galore -q 25 --illumina --gzip --length 35 ${fq1}
mv ${r1base}_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz
cp ${pair_id}.trim.R1.fastq.gz ${pair_id}.trim.R2.fastq.gz
fi
because the user's fastq file names are in a format of 'SampleID_ReplicateNumber_ReadNumber.fq.gz', e.g. 'ff_Cre_1_1.fq.gz'. In this case 'r1base' and 'r2base' are invalid.https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/10Update script to incorrpoarte chagnes from ChiP_seq pipeline2019-12-03T10:27:14-06:00Venkat MalladiUpdate script to incorrpoarte chagnes from ChiP_seq pipelineUpdate scripts to include changes to sample names and outputfolderUpdate scripts to include changes to sample names and outputfolderVersion 1.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/9Add in references and version used in script2020-05-28T13:58:53-05:00Venkat MalladiAdd in references and version used in scriptVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/8Make ATAC-seq pipeline generalizibe for Open Chromatin2019-12-03T10:26:25-06:00Venkat MalladiMake ATAC-seq pipeline generalizibe for Open ChromatinVersion 1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/7Shift is incorrect for ATAC-seq2020-01-06T13:57:44-06:00Venkat MalladiShift is incorrect for ATAC-seqShift should be switchted in call_peaks_macs2.py
`--shift 73 --extsize %s`
shift 37 and extsize 73Shift should be switchted in call_peaks_macs2.py
`--shift 73 --extsize %s`
shift 37 and extsize 73Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/12Fix dea.R2019-04-29T10:57:45-05:00Jonathan GesellFix dea.RCorrect link to corrected dea.R scriptCorrect link to corrected dea.R scriptJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/3Add Jon's ORCID2019-04-29T10:31:17-05:00Venkat MalladiAdd Jon's ORCIDVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/24Organize output folders2019-05-03T21:47:00-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduOrganize output folderseg check design into misc foldereg check design into misc folderv1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/23CI: mkdir ln forcing2019-08-15T00:30:07-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCI: mkdir ln forcingmkdir -p
ln -sfnmkdir -p
ln -sfnv1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/2Document Backups2019-04-26T23:26:57-05:00Venkat MalladiDocument BackupsVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/22Make changelog2019-08-15T00:30:07-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMake changelogv1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/21Change regex in astrocyte yaml2019-08-15T00:30:07-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduChange regex in astrocyte yamlrelated to BICF/Astrocyte/cellranger_mkfastq#16related to BICF/Astrocyte/cellranger_mkfastq#16v1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/20CI: Make Astrocyte test only one for tag2019-05-24T14:17:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCI: Make Astrocyte test only one for tagv1.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/19Move params out of main.nf2019-04-26T15:47:15-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove params out of main.nfGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/20Add DOI2019-08-15T00:29:22-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd DOIASAPASAPv1.1.0Venkat MalladiVenkat Malladi2019-04-29https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/18Add DOI2019-04-27T13:11:57-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd DOIWait for 1.1.4 to hit production AstrocyteWait for 1.1.4 to hit production Astrocytev1.2.0Venkat MalladiVenkat Malladi2019-04-22https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/17Link changelog to index.md2019-05-24T14:17:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduLink changelog to index.mdv1.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/1RNAseq-ProcessScripts2019-04-26T11:07:33-05:00Holly RuessRNAseq-ProcessScriptsWrite instructions on how to make changes to the processScripts for the RNAseq pipeline and link them together in the RNAseq branchWrite instructions on how to make changes to the processScripts for the RNAseq pipeline and link them together in the RNAseq branchHolly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/16Add "." to regex for Astrocyte file input2019-05-24T14:17:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd "." to regex for Astrocyte file input```
.*\.tar*
.*\.csv
```
not working```
.*\.tar*
.*\.csv
```
not workingv1.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/15Fix astrocyte regex2019-04-26T01:34:28-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix astrocyte regex```
regex: ".*csv"
```
to
```
regex: "*.csv"
``````
regex: ".*csv"
```
to
```
regex: "*.csv"
```v1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu