Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Allan's changes to nf-core #1

Draft
wants to merge 68 commits into
base: nfcore_master
Choose a base branch
from
Draft

Allan's changes to nf-core #1

wants to merge 68 commits into from

Conversation

y-popov
Copy link
Contributor

@y-popov y-popov commented Oct 25, 2023

No description provided.

@Sanger-ad7
changed runtimes in conf
658805e
@Sanger-ad7
increased job timeout
cdd0929
@Sanger-ad7
Added Reference dict to schema
e457e5e
@Sanger-ad7
Removed dict from schema
fc4e2fe
@Sanger-ad7
added singularity settings to config
1e39764
@Sanger-ad7
added singularity cacheDir to config
1e188be
@Sanger-ad7
added LSF, errorStrategy, cache and Retry setting to base.config
2b1c59c
@Sanger-ad7
Commented out time from config
7ec0642
@Sanger-ad7
Commented out process_long from config
dcd9784
@Sanger-ad7
Added java setting for serial GC
ace8a64
@Sanger-ad7
Changed GATK4processes to use 1 cpu and 8G mem initially
f4aa365
@Sanger-ad7
changed config to run importgvcf and genotypegvcf in baasement
0e9f3cc
@Sanger-ad7
Altered genomicdbimport for running on node /tmp
4d230df
@Sanger-ad7
escaped some $ signs
fe1a884
@Sanger-ad7
Modified genomicsdbimport module
9827477
@Sanger-ad7
Added /tmp to singulartiy bind
b709d2c
@Sanger-ad7
removed tmp-dir from command
d6816df
@Sanger-ad7
Altered modules to use genDB on /tmp
5756e83
@Sanger-ad7
Fixed genotypegvcfs module
4f805e8
@Sanger-ad7
Changed gendb name
3dedf87
@Sanger-ad7
Corrected --variant parameter
ca8c1e3
@Sanger-ad7
Updated vcftools singularity image
179149c
@Sanger-ad7
Turned off vcftools due to error
e2d3362
@Sanger-ad7
changed config back
6d775ad
@Sanger-ad7
Tried to fix vcftools countTsTv non-zero exit
11b4bf6
@Sanger-ad7
Tried to fix vcftools countTsTv non-zero exit again
8b825b6
@Sanger-ad7
Modified schema for dict file, optimised bed intervals
ba4e1fe
@Sanger-ad7
Added a few more settings for Allele Specific VQSR
35a0778
@Sanger-ad7
changed schema back to before
4696dff
@Sanger-ad7
changed schema to show dict
2be7c16
Sanger-ad7 added 28 commits July 11, 2023 16:25
@Sanger-ad7
Added description of intervals to use
4a2bc15
@Sanger-ad7
Corrected format in lsf.conf
5ffab0a
@Sanger-ad7
Made joint call default
4ae842e
@Sanger-ad7
Made joint call default
6f67ddb
@Sanger-ad7
Made joint call default
7b9698c
@Sanger-ad7
Made joint call default
103ff6b
@Sanger-ad7
Made joint call default
00fe590
@Sanger-ad7
schema change
ad57276
@Sanger-ad7
schema change
89f7281
@Sanger-ad7
changed nucleotides per second default
4b4f6ef
@Sanger-ad7
changed nucleotides per second default
1f102af
@Sanger-ad7
changed nucleotides per second default in test_full_germline.config
2fcc82d
@Sanger-ad7
Publish GVCF while joint calling
9c2ac27
@Sanger-ad7
Merge vcf even if joint calling
3db3362
@Sanger-ad7
removed GATK_SINGLE_SAMPLE_GERMLINE_VARIANT_CALLING from haplotypecaller
6b54d73
@Sanger-ad7
Deleted VQSR MERGE and output after ApplyVQSR of indels to snpVQSR input
a02418b
@Sanger-ad7
Reverted Deletion of VQSR MERGE
0a21435
@Sanger-ad7
made snp applyvqsr the input for indel applyvqsr
7e71c45
@Sanger-ad7
made snp applyvqsr the input for indel applyvqsr
97729cb
@Sanger-ad7
Trying to get applyVQSR to work for indels
5605ad2
@Sanger-ad7
incorporated changes to avoid VQSR duplications
b39dc4d
@Sanger-ad7
Removed VCF filtering
42d46f8
@Sanger-ad7
Fixed edit error
e3cc2b3
@Sanger-ad7
Fixed output variable
0963b35
@Sanger-ad7
Changed config to publish VQSR from APPLYVQSR_INDEl
bc720e4
@Sanger-ad7
Added variantrecalibrator plot and publish
af33661
@Sanger-ad7
Changed publish pattern
d2339ac
@Sanger-ad7
Added pdf emit to variantrecalibrator
ce60ca2
@y-popov y-popov changed the title HGI changes to nf-core Allan's changes to nf-core Oct 30, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@y-popov @Sanger-ad7