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

Patch 2.3.2 #461

Merged
merged 6 commits into from
Jun 23, 2023
Merged

Patch 2.3.2 #461

Show file tree
Hide file tree
Changes from 4 commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
b9b9b4b
Fix patchs in full tests config
jfy133 Jun 21, 2023
0c47530
Fix overwriting of pydamage output
jfy133 Jun 21, 2023
3a2f104
Update CHANGELOG.md
jfy133 Jun 21, 2023
c43e47d
Update nextflow.config
jfy133 Jun 21, 2023
0d4c335
Update CHANGELOG.md
jfy133 Jun 22, 2023
3499ce0
Update CHANGELOG.md
jfy133 Jun 22, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,13 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v2.3.2 - [2023-06-21]
jfy133 marked this conversation as resolved.
Show resolved Hide resolved

### `Fixed`

- [#461](https://github.com/nf-core/mag/pull/461) - Fix full-size AWS test profile paths (by @jfy133)
- [#461](https://github.com/nf-core/mag/pull/461) - Fix pyDamage results being overwritten (reported by @alexhbnr, fix by @jfy133)

## v2.3.1 - [2023-06-19]

### `Fixed`
Expand Down
4 changes: 2 additions & 2 deletions conf/modules.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -496,7 +496,7 @@ process {
withName: PYDAMAGE_ANALYZE {
ext.prefix = { "${meta.assembler}-${meta.id}" }
publishDir = [
path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/" },
path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.assembler}-${meta.id}/" },
mode: params.publish_dir_mode
]
}
Expand All @@ -505,7 +505,7 @@ process {
ext.prefix = { "${meta.assembler}-${meta.id}" }
ext.args = "-t ${params.pydamage_accuracy}"
publishDir = [
path: {"${params.outdir}/Ancient_DNA/pydamage/filter/" },
path: {"${params.outdir}/Ancient_DNA/pydamage/filter/${meta.assembler}-${meta.id}/" },
mode: params.publish_dir_mode
]
}
Expand Down
17 changes: 11 additions & 6 deletions conf/test_full.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,19 +10,21 @@
----------------------------------------------------------------------------------------
*/

cleanup = true
d4straub marked this conversation as resolved.
Show resolved Hide resolved

params {
config_profile_name = 'Full test profile'
config_profile_description = 'Full test dataset to check pipeline function'

// Input data for full size test
// hg19 reference with highly conserved and low-complexity regions masked by Brian Bushnell
host_fasta = "s3://nf-core-awsmegatests/mag/input_data/hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz"
input = "s3://nf-core-awsmegatests/mag/input_data/samplesheets/samplesheet.full.csv"
host_fasta = "s3://ngi-igenomes/test-data/mag/hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz"
input = "s3://ngi-igenomes/test-data/mag/samplesheets/samplesheet.full.csv"

centrifuge_db = "s3://nf-core-awsmegatests/mag/input_data/p_compressed+h+v.tar.gz"
kraken2_db = "s3://nf-core-awsmegatests/mag/input_data/minikraken_8GB_202003.tgz"
cat_db = "s3://nf-core-awsmegatests/mag/input_data/CAT_prepare_20210107.tar.gz"
gtdb = "s3://nf-core-awsmegatests/mag/input_data/gtdbtk_r202_data.tar.gz"
centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz"
kraken2_db = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz"
cat_db = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz"
gtdb = "s3://ngi-igenomes/test-data/mag/gtdbtk_r202_data.tar.gz"

// reproducibility options for assembly
spades_fix_cpus = 10
Expand All @@ -33,4 +35,7 @@ params {

// test CAT with official taxonomic ranks only
cat_official_taxonomy = true

// Skip CONCOCT due to timeout issues
skip_concoct = true
}
2 changes: 1 addition & 1 deletion nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -308,7 +308,7 @@ manifest {
description = """Assembly, binning and annotation of metagenomes"""
mainScript = 'main.nf'
nextflowVersion = '!>=22.10.1'
version = '2.3.1'
version = '2.3.2'
doi = '10.1093/nargab/lqac007'
}

Expand Down