s-andrews nextflow_pipelines issues

s-andrews / nextflow_pipelines

The set of NGS processing pipelines used at Babraham

GNU General Public License v3.0

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issues

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Trim galore is unnecessarily slow and doesn't parallelise

#43 s-andrews closed 5 months ago
3
Add in updates to TrAEL-seq pipeline from main branch

#42 laurabiggins closed 5 months ago
0
Executor overcommits on slurm systems with hyperthreading

#41 s-andrews closed 5 months ago
1
Trael updates

#40 laurabiggins closed 1 year ago
0
Requirement for this pipeline?

#39 ShouWenWang closed 5 months ago
1
Override options don't always take

#38 s-andrews opened 2 years ago
0
MultiQC report on rnaseq pipeline gets default name

#37 s-andrews closed 2 years ago
2
Trael seq pipeline broken due to changes in TrAELseq_sequence_based_deduplication.py

#36 s-andrews opened 2 years ago
0
trael seq pipeline still has the help from the ChIP-seq pipeline

#35 s-andrews opened 2 years ago
0
Update some pipelines

#34 FelixKrueger closed 2 years ago
0
Added GRCh38 primary assembly

#33 FelixKrueger closed 2 years ago
0
removed param --fastqs. --fastqs_dir it needed.

#32 FelixKrueger closed 2 years ago
0
Cellranger also executes

#31 FelixKrueger closed 2 years ago
0
Updating cellranger count process

#30 FelixKrueger closed 2 years ago
0
Pipelines fail on filenames containing a + symbol

#29 s-andrews opened 2 years ago
4
Added circular spike-in to yeast genome

#28 FelixKrueger closed 2 years ago
0
Added Cellranger count pipeline

#27 FelixKrueger closed 3 years ago
0
reStrainingOrder had stopped working due to input tuples

#26 FelixKrueger closed 3 years ago
0
This PR fixes the file recognition of Trim Galore trimmed input files

#25 FelixKrueger closed 3 years ago
0
Update and fixes

#24 FelixKrueger closed 3 years ago
0
EF genome broken for hisat2?

#23 s-andrews closed 3 years ago
1
Adding a TrAEL-seq pipeline

#22 FelixKrueger closed 3 years ago
0
Added PBAT Dirty Harry pipeline

#21 FelixKrueger closed 3 years ago
0
Added reStrainingOrder pipeline

#20 FelixKrueger closed 3 years ago
0
Clean up work folder unless something fails

#19 s-andrews opened 3 years ago
0
Adding initial Samtools functionality

#18 FelixKrueger closed 3 years ago
0
Add sort and index BAM pipeline

#17 FelixKrueger closed 3 years ago
0
Incorrect detection of paired end data

#16 s-andrews opened 3 years ago
4
Major usability update for Babraham pipelines

#15 FelixKrueger closed 4 years ago
2
Added dynamic retries with backoff for several modules

#14 FelixKrueger closed 4 years ago
0
Adapting to DSL2 changes in 20.07 release candidate

#13 FelixKrueger closed 4 years ago
0
Only concordant PE alignments for Bowtie2

#12 FelixKrueger closed 4 years ago
0
[Reminder:] position of args in nf command matters with flags such as --single_end

#11 FelixKrueger closed 4 years ago
1
Warning message from nf_qc

#10 s-andrews closed 4 years ago
2
Pipelines don't work with uncompressed fastq files

#9 s-andrews opened 4 years ago
0
Some changes for demo

#8 FelixKrueger closed 4 years ago
0
Added list genome functionality to all pipelines

#7 FelixKrueger closed 4 years ago
0
Files module also handles Trim Galore paired-end input

#6 FelixKrueger closed 4 years ago
0
Updated code, added --single_end mode and added UmiBam

#5 FelixKrueger closed 4 years ago
0
Changed email settings and added MultiQC to QC pipeline

#4 FelixKrueger closed 4 years ago
0
Update to the most recent set of nf pipelines

#3 FelixKrueger closed 4 years ago
0
Update our set of Nextflow pipelines and modules

#2 FelixKrueger closed 4 years ago
0
Merge pull request #1 from s-andrews/master

#1 FelixKrueger closed 4 years ago
0