diff --git a/CHANGELOG.md b/CHANGELOG.md
index 27150aa..e9a045c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,14 @@
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).
+## 1.1.2 - canguro
+
+This release reverts the `wfmash` tool version to 0.10.4, because the current releases are unstable, not documented, and I don't understand how to set the parameters properly.
+It is currently unclear, when a new _stable_ release will become available. @baozg or @AndreaGuarracino are evaluating.
+
+- Per default, we set the number of mappings in `wfmash` to `--n_haplotypes - 1`. Previously, this was set to `1`.
+- Deactivated parameter `wfmash_hg_filter_ani_diff`, because the older `wfmash` version does not support it.
+
## 1.1.1 - LATÜRNICH
This release fixes some important bugs:
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index c6b5600..31ab221 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
report_comment: >
- This report has been generated by the nf-core/pangenome
+ This report has been generated by the nf-core/pangenome
analysis pipeline. For information about how to interpret these results, please see the
- documentation.
+ documentation.
report_section_order:
"nf-core-pangenome-methods-description":
order: -1000
diff --git a/conf/modules.config b/conf/modules.config
index c5dc2c4..b4dcdf3 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -102,7 +102,7 @@ process {
withName: WFMASH_MAP_ALIGN {
ext.args = {
[
- "-n ${params.wfmash_n_mappings}",
+ params.wfmash_n_mappings ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}",
"-s ${parse_int(params.wfmash_segment_length)}",
"-p ${params.wfmash_map_pct_id}",
params.wfmash_merge_segments ? "-M" : "",
@@ -113,8 +113,8 @@ process {
"-H ${params.wfmash_mash_kmer_thres}",
"${wfmash_sparse_map_cmd}",
params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "",
- "-2 ${params.wfmash_hg_filter_ani_diff}",
- "--lower-triangular",
+// "-2 ${params.wfmash_hg_filter_ani_diff}",
+// "--lower-triangular",
].join(" ").trim()
}
publishDir = [
@@ -127,7 +127,7 @@ process {
withName: WFMASH_MAP {
ext.args = {
[
- "-n ${params.wfmash_n_mappings}",
+ params.wfmash_n_mappings ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}",
"-s ${parse_int(params.wfmash_segment_length)}",
"-p ${params.wfmash_map_pct_id}",
params.wfmash_merge_segments ? "-M" : "",
@@ -139,8 +139,8 @@ process {
"${wfmash_sparse_map_cmd}",
params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "",
"-m",
- "-2 ${params.wfmash_hg_filter_ani_diff}",
- "--lower-triangular",
+// "-2 ${params.wfmash_hg_filter_ani_diff}",
+// "--lower-triangular",
].join(" ").trim()
}
publishDir = [
@@ -153,7 +153,7 @@ process {
withName: WFMASH_MAP_COMMUNITY {
ext.args = {
[
- "-n ${params.wfmash_n_mappings}",
+ params.wfmash_n_mappings ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}",
"-s ${parse_int(params.wfmash_segment_length)}",
"-p ${params.wfmash_map_pct_id}",
params.wfmash_merge_segments ? "-M" : "",
@@ -165,8 +165,8 @@ process {
"${wfmash_sparse_map_cmd}",
params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "",
"-m",
- "-2 ${params.wfmash_hg_filter_ani_diff}",
- "--lower-triangular",
+// "-2 ${params.wfmash_hg_filter_ani_diff}",
+// "--lower-triangular",
].join(" ").trim()
}
publishDir = [
@@ -188,7 +188,7 @@ process {
withName: WFMASH_ALIGN {
ext.args = {
[
- "-n ${params.wfmash_n_mappings}",
+ params.wfmash_n_mappings ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}",
"-s ${parse_int(params.wfmash_segment_length)}",
"-p ${params.wfmash_map_pct_id}",
params.wfmash_merge_segments ? "-M" : "",
@@ -200,8 +200,8 @@ process {
"${wfmash_sparse_map_cmd}",
params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "",
"--invert-filtering",
- "-2 ${params.wfmash_hg_filter_ani_diff}",
- "--lower-triangular",
+// "-2 ${params.wfmash_hg_filter_ani_diff}",
+// "--lower-triangular",
].join(" ").trim()
}
publishDir = [
diff --git a/modules.json b/modules.json
index eecc70e..134e870 100644
--- a/modules.json
+++ b/modules.json
@@ -82,7 +82,7 @@
},
"wfmash": {
"branch": "master",
- "git_sha": "0c49f318ec4701b891a87f25fb07b34713c90203",
+ "git_sha": "77c0c76b7eb7ec564617e635953addc9fb40b61e",
"installed_by": ["modules"]
}
}
diff --git a/modules/nf-core/wfmash/environment.yml b/modules/nf-core/wfmash/environment.yml
deleted file mode 100644
index 071aa5a..0000000
--- a/modules/nf-core/wfmash/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: wfmash
-channels:
- - conda-forge
- - bioconda
- - defaults
-dependencies:
- - bioconda::wfmash=0.12.6
diff --git a/modules/nf-core/wfmash/main.nf b/modules/nf-core/wfmash/main.nf
index 7c64148..33c556a 100644
--- a/modules/nf-core/wfmash/main.nf
+++ b/modules/nf-core/wfmash/main.nf
@@ -2,10 +2,10 @@ process WFMASH {
tag "$meta.id"
label 'process_medium'
- conda "${moduleDir}/environment.yml"
+ conda "bioconda::wfmash=0.10.4"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/wfmash:0.12.6--h11f254b_0':
- 'biocontainers/wfmash:0.12.6--h11f254b_0' }"
+ 'https://depot.galaxyproject.org/singularity/wfmash:0.10.4--hea8008d_0':
+ 'biocontainers/wfmash:0.10.4--hea8008d_0' }"
input:
tuple val(meta), path(fasta_gz), path(paf), path(gzi), path(fai)
diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml
index dc5cd5a..80e630c 100644
--- a/modules/nf-core/wfmash/meta.yml
+++ b/modules/nf-core/wfmash/meta.yml
@@ -13,7 +13,8 @@ tools:
documentation: https://github.com/waveygang/wfmash
tool_dev_url: https://github.com/waveygang/wfmash
doi: 10.5281/zenodo.6949373
- licence: ["MIT"]
+ licence: "['MIT']"
+
input:
- meta:
type: map
@@ -43,6 +44,7 @@ input:
type: file
description: Optional inpute file in FASTA format specifying the query sequences as a list.
pattern: "*.{fa,fna,fasta}"
+
output:
- meta:
type: map
@@ -57,7 +59,6 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
+
authors:
- "@subwaystation"
-maintainers:
- - "@subwaystation"
diff --git a/modules/nf-core/wfmash/tests/main.nf.test b/modules/nf-core/wfmash/tests/main.nf.test
deleted file mode 100644
index 41d8c23..0000000
--- a/modules/nf-core/wfmash/tests/main.nf.test
+++ /dev/null
@@ -1,39 +0,0 @@
-nextflow_process {
-
- name "Test Process WFMASH"
- script "../main.nf"
- process "WFMASH"
- config "./nextflow.config"
-
- tag "modules"
- tag "modules_nfcore"
- tag "wfmash"
-
- test("homo_sapiens - pangenome - pangenome_fa_bgzip") {
-
- when {
- process {
- """
- input[0] = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip'], checkIfExists: true),
- [], // empty paf input
- file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip_gzi'], checkIfExists: true), // gzi
- file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip_fai'], checkIfExists: true) // fai
- ]
- input[1] = true // empty paf input
- input[2] = []
- """
- }
- }
-
- then {
- assertAll(
- { assert process.success },
-// { assert snapshot(process.out).exists() } // if run on more than 1 thread the lines in the resulting PAF will appear in a different order
- )
- }
-
- }
-
-}
diff --git a/modules/nf-core/wfmash/tests/main.nf.test.snap b/modules/nf-core/wfmash/tests/main.nf.test.snap
deleted file mode 100644
index 97a51e4..0000000
--- a/modules/nf-core/wfmash/tests/main.nf.test.snap
+++ /dev/null
@@ -1,33 +0,0 @@
-{
- "homo_sapiens - pangenome - pangenome_fa_bgzip": {
- "content": [
- {
- "0": [
- [
- {
- "id": "test",
- "single_end": false
- },
- "test.paf:md5,aa6629548e32b2d036c0767c9086a6dd"
- ]
- ],
- "1": [
- "versions.yml:md5,0da45b7a6424a967e2f39225fb020140"
- ],
- "paf": [
- [
- {
- "id": "test",
- "single_end": false
- },
- "test.paf:md5,aa6629548e32b2d036c0767c9086a6dd"
- ]
- ],
- "versions": [
- "versions.yml:md5,0da45b7a6424a967e2f39225fb020140"
- ]
- }
- ],
- "timestamp": "2024-01-25T15:12:21.284828212"
- }
-}
\ No newline at end of file
diff --git a/modules/nf-core/wfmash/tests/nextflow.config b/modules/nf-core/wfmash/tests/nextflow.config
deleted file mode 100644
index b7e9c98..0000000
--- a/modules/nf-core/wfmash/tests/nextflow.config
+++ /dev/null
@@ -1,12 +0,0 @@
-process {
-
- withName: WFMASH {
- ext.args = {
- [
- "-s 500", // necessary because of https://github.com/waveygang/wfmash/issues/218
- "-X"
- ].join(" ").trim()
- }
- }
-
-}
diff --git a/modules/nf-core/wfmash/tests/tags.yml b/modules/nf-core/wfmash/tests/tags.yml
deleted file mode 100644
index 7001b08..0000000
--- a/modules/nf-core/wfmash/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-wfmash:
- - "modules/nf-core/wfmash/**"
diff --git a/nextflow.config b/nextflow.config
index ec06325..3d10ac9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -27,7 +27,7 @@ params {
wfmash_only = false
wfmash_temp_dir = null
wfmash_hg_filter_ani_diff = 30
- wfmash_n_mappings = 1
+ wfmash_n_mappings = null
// Seqwish options
seqwish_paf = null
@@ -277,7 +277,7 @@ manifest {
description = """The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
- version = '1.1.1'
+ version = '1.1.2'
doi = 'https://doi.org/10.5281/zenodo.8202636'
}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index ab4f48d..38238b7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -122,8 +122,7 @@
},
"wfmash_n_mappings": {
"type": "integer",
- "default": 1,
- "description": "Number of mappings for each segment."
+ "description": "Number of mappings for each segment. [default: `n_haplotypes - 1`]."
}
}
},