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Update ampcombi 2.0.1 #7142

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merged 18 commits into from
Dec 11, 2024
Merged

Update ampcombi 2.0.1 #7142

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96ac596
update ampcombi to 2.0.1
Darcy220606 Dec 2, 2024
7fa49b9
Merge branch 'nf-core:master' into update_ampcombi2.0.1
Darcy220606 Dec 2, 2024
df8cdc7
update the rest of the submodules to 2.0.1
Darcy220606 Dec 3, 2024
7a3c105
add dir_path as input in parsetables
Darcy220606 Dec 3, 2024
32b192e
Merge branch 'nf-core:master' into update_ampcombi2.0.1
Darcy220606 Dec 3, 2024
90523c2
Nextflow format document
Darcy220606 Dec 4, 2024
b965c7c
add code review
Darcy220606 Dec 4, 2024
ae1dab8
fix harshil alignment
Darcy220606 Dec 4, 2024
1658e58
remove binary files emmition
Darcy220606 Dec 5, 2024
ad367f1
Merge branch 'master' into update_ampcombi2.0.1
Darcy220606 Dec 5, 2024
fb21d92
add interpro optional input
Darcy220606 Dec 11, 2024
106c802
Merge branch 'master' into update_ampcombi2.0.1
Darcy220606 Dec 11, 2024
62a8c7d
format document
Darcy220606 Dec 11, 2024
55c13ab
Merge branch 'update_ampcombi2.0.1' of https://github.com/Darcy220606…
Darcy220606 Dec 11, 2024
8b9a95a
fix container versions
Darcy220606 Dec 11, 2024
98c9974
add minor code review
Darcy220606 Dec 11, 2024
27f3867
Merge branch 'nf-core:master' into update_ampcombi2.0.1
Darcy220606 Dec 11, 2024
70839c7
add more code reviews :)
Darcy220606 Dec 11, 2024
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2 changes: 1 addition & 1 deletion modules/nf-core/ampcombi2/cluster/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::ampcombi=0.2.2"
- "bioconda::ampcombi=2.0.1"
4 changes: 2 additions & 2 deletions modules/nf-core/ampcombi2/cluster/main.nf
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Expand Up @@ -4,8 +4,8 @@ process AMPCOMBI2_CLUSTER {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ampcombi:0.2.2--pyhdfd78af_0':
'biocontainers/ampcombi:0.2.2--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
'biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"

input:
path(summary_file)
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18 changes: 9 additions & 9 deletions modules/nf-core/ampcombi2/cluster/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -4,14 +4,14 @@
true,
true,
[
"versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
"versions.yml:md5,b629089d44775078dce5e664a455422b"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-04-24T12:11:40.928513749"
"timestamp": "2024-12-03T07:57:01.869983435"
},
"ampcombi2_cluster - metagenome - stub": {
"content": [
Expand All @@ -26,7 +26,7 @@
"Ampcombi_cluster.log:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"3": [
"versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
"versions.yml:md5,b629089d44775078dce5e664a455422b"
],
"cluster_tsv": [
"Ampcombi_summary_cluster.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
Expand All @@ -38,14 +38,14 @@
"Ampcombi_summary_cluster_representative_seq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"versions": [
"versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
"versions.yml:md5,b629089d44775078dce5e664a455422b"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-04-24T12:12:08.780718892"
"timestamp": "2024-12-03T07:57:23.939137628"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/ampcombi2/complete/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::ampcombi=0.2.2"
- "bioconda::ampcombi=2.0.1"
4 changes: 2 additions & 2 deletions modules/nf-core/ampcombi2/complete/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process AMPCOMBI2_COMPLETE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ampcombi:0.2.2--pyhdfd78af_0':
'biocontainers/ampcombi:0.2.2--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
'biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"

input:
path(summaries)
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24 changes: 12 additions & 12 deletions modules/nf-core/ampcombi2/complete/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -6,39 +6,39 @@
"Ampcombi_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"1": [

],
"2": [
"versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
"versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
],
"log": [

],
"tsv": [
"Ampcombi_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"versions": [
"versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
"versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-04-29T11:55:16.030399422"
"timestamp": "2024-12-03T07:57:53.385349848"
},
"ampcombi2_complete - contigs": {
"content": [
true,
[
"versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
"versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-04-29T11:54:54.334224301"
"timestamp": "2024-12-03T07:57:40.263912946"
}
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/ampcombi2/parsetables/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::ampcombi=0.2.2"
- "bioconda::ampcombi=2.0.1"
74 changes: 45 additions & 29 deletions modules/nf-core/ampcombi2/parsetables/main.nf
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Original file line number Diff line number Diff line change
@@ -1,47 +1,56 @@
process AMPCOMBI2_PARSETABLES {
tag "$meta.id"
tag "${meta.id}"
label 'process_medium'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ampcombi:0.2.2--pyhdfd78af_0':
'biocontainers/ampcombi:0.2.2--pyhdfd78af_0' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0'
: 'biocontainers/ampcombi:2.0.1--pyhdfd78af_0'}"

input:
tuple val(meta), path(amp_input)
path(faa_input)
path(gbk_input)
path(opt_amp_db)
path faa_input
path gbk_input
val opt_amp_db
path opt_amp_db_dir

output:
tuple val(meta), path("${meta.id}/") , emit: sample_dir
tuple val(meta), path("${meta.id}/contig_gbks/") , emit: contig_gbks
tuple val(meta), path("${meta.id}/${meta.id}_diamond_matches.txt"), emit: txt
tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.tsv") , emit: tsv
tuple val(meta), path("${meta.id}/${meta.id}_amp.faa") , emit: faa
tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.log") , emit: sample_log, optional:true
tuple val(meta), path("Ampcombi_parse_tables.log") , emit: full_log, optional:true
tuple val(meta), path("amp_ref_database/") , emit: results_db, optional:true
tuple val(meta), path("amp_ref_database/*.dmnd") , emit: results_db_dmnd, optional:true
tuple val(meta), path("amp_ref_database/*.clean.fasta") , emit: results_db_fasta, optional:true
tuple val(meta), path("amp_ref_database/*.tsv") , emit: results_db_tsv, optional:true
path "versions.yml" , emit: versions
tuple val(meta), path("${meta.id}/") , emit: sample_dir
tuple val(meta), path("${meta.id}/contig_gbks/") , emit: contig_gbks
tuple val(meta), path("${meta.id}/${meta.id}_mmseqs_matches.tsv") , emit: db_tsv
tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.tsv") , emit: tsv
tuple val(meta), path("${meta.id}/${meta.id}_amp.faa") , emit: faa
tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.log") , emit: sample_log , optional:true
tuple val(meta), path("Ampcombi_parse_tables.log") , emit: full_log , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/") , emit: db , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/*.txt") , emit: db_txt , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/*.fasta") , emit: db_fasta , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/mmseqs2/") , emit: db_mmseqs , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/mmseqs2/ref_DB") , emit: db_mmseqs_binary , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/mmseqs2/ref_DB.dbtype") , emit: db_mmseqs_dbtype , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/mmseqs2/ref_DB_h") , emit: db_mmseqs_h , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/mmseqs2/ref_DB_h.dbtype"), emit: db_mmseqs_hdbtype , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/mmseqs2/ref_DB_h.index") , emit: db_mmseqs_hindex , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/mmseqs2/ref_DB.index") , emit: db_mmseqs_index , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/mmseqs2/ref_DB.lookup") , emit: db_mmseqs_lookup , optional:true
tuple val(meta), path("amp_${opt_amp_db}_database/mmseqs2/ref_DB.source") , emit: db_mmseqs_source , optional:true
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path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def db = opt_amp_db? "--amp_database $opt_amp_db": ""
"""
ampcombi parse_tables \\
--path_list '${amp_input.collect{"$it"}.join("' '")}' \\
--path_list '${amp_input.collect { "${it}" }.join("' '")}' \\
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--faa ${faa_input} \\
--gbk ${gbk_input} \\
--sample_list ${prefix} \\
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${db} \\
$args \\
--amp_database ${opt_amp_db} \\
--amp_database_dir ${opt_amp_db_dir} \\
${args} \\
--threads ${task.cpus}

cat <<-END_VERSIONS > versions.yml
Expand All @@ -53,20 +62,27 @@ process AMPCOMBI2_PARSETABLES {
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def db = opt_amp_db? "--amp_database $opt_amp_db": ""
"""
mkdir -p ${prefix}
mkdir -p ${prefix}/contig_gbks
touch ${prefix}/${meta.id}_diamond_matches.txt
touch ${prefix}/${meta.id}_mmseqs_matches.tsv
touch ${prefix}/${meta.id}_ampcombi.tsv
touch ${prefix}/${meta.id}_amp.faa
touch ${prefix}/${meta.id}_ampcombi.log
touch Ampcombi_parse_tables.log

mkdir -p amp_ref_database
touch amp_ref_database/*.dmnd
touch amp_ref_database/*.clean.fasta
touch amp_ref_database/*.tsv
mkdir -p amp_${opt_amp_db}_database
mkdir -p amp_${opt_amp_db}_database/mmseqs2
touch amp_${opt_amp_db}_database/*.fasta
touch amp_${opt_amp_db}_database/*.txt
touch amp_${opt_amp_db}_database/mmseqs2/ref_DB
touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.dbtype
touch amp_${opt_amp_db}_database/mmseqs2/ref_DB_h
touch amp_${opt_amp_db}_database/mmseqs2/ref_DB_h.dbtype
touch amp_${opt_amp_db}_database/mmseqs2/ref_DB_h.index
touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.index
touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.lookup
touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.source

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
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