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diann 1.8.1 -> 1.9.1dev #381

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diann 1.8.1 -> 1.9.1dev #381

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b57961a
diann 1.8.1 -> 1.9.1dev
ypriverol Jul 1, 2024
766ffc3
diann 1.8.1 -> 1.9.1dev
ypriverol Jul 2, 2024
6317c6b
diann 1.8.1 -> 1.9.1dev
ypriverol Jul 2, 2024
9cb3922
diann 1.8.1 -> 1.9.1dev
ypriverol Jul 2, 2024
96d1d1c
diann 1.8.1 -> 1.9.1dev
ypriverol Jul 2, 2024
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2 changes: 1 addition & 1 deletion bin/diann_convert.py
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Expand Up @@ -292,7 +292,7 @@ def diann_version(self) -> str:
return diann_version_id

def validate_diann_version(self) -> None:
supported_diann_versions = ["1.8.1"]
supported_diann_versions = ["1.8.1", "1.9.beta.1"]
if self.diann_version not in supported_diann_versions:
raise ValueError(f"Unsupported DIANN version {self.diann_version}")

Expand Down
6 changes: 3 additions & 3 deletions modules/local/assemble_empirical_library/main.nf
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Expand Up @@ -3,8 +3,8 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
label 'process_low'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
'docker.io/biocontainers/diann:v1.8.1_cv1' }"
'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' :
'ghcr.io/bigbio/diann:1.9.1dev' }"

input:
// In this step the real files are passed, and not the names
Expand Down Expand Up @@ -58,7 +58,7 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?")
END_VERSIONS
"""
}
6 changes: 3 additions & 3 deletions modules/local/diann_preliminary_analysis/main.nf
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Expand Up @@ -3,8 +3,8 @@ process DIANN_PRELIMINARY_ANALYSIS {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
'docker.io/biocontainers/diann:v1.8.1_cv1' }"
'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' :
'ghcr.io/bigbio/diann:1.9.1dev' }"

input:
tuple val(meta), path(ms_file), path(predict_library)
Expand Down Expand Up @@ -61,7 +61,7 @@ process DIANN_PRELIMINARY_ANALYSIS {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?")
END_VERSIONS
"""
}
9 changes: 5 additions & 4 deletions modules/local/diannsummary/main.nf
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Expand Up @@ -3,8 +3,8 @@ process DIANNSUMMARY {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
'docker.io/biocontainers/diann:v1.8.1_cv1' }"
'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' :
'ghcr.io/bigbio/diann:1.9.1dev' }"

input:
// Note that the files are passed as names and not paths, this prevents them from being staged
Expand All @@ -24,7 +24,8 @@ process DIANNSUMMARY {
path "diann_report.gg_matrix.tsv", emit: gg_matrix
path "diann_report.unique_genes_matrix.tsv", emit: unique_gene_matrix
path "diannsummary.log", emit: log
path "empirical_library.tsv.speclib", emit: final_speclib
path "empirical_library.tsv", emit: final_speclib
path "empirical_library.tsv.skyline.speclib", emit: skyline_speclib
path "versions.yml", emit: version

when:
Expand Down Expand Up @@ -69,7 +70,7 @@ process DIANNSUMMARY {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?")
END_VERSIONS
"""
}
6 changes: 3 additions & 3 deletions modules/local/individual_final_analysis/main.nf
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Expand Up @@ -3,8 +3,8 @@ process INDIVIDUAL_FINAL_ANALYSIS {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
'docker.io/biocontainers/diann:v1.8.1_cv1' }"
'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' :
'ghcr.io/bigbio/diann:1.9.1dev' }"

input:
tuple val(meta), path(ms_file), path(fasta), path(diann_log), path(library)
Expand Down Expand Up @@ -53,7 +53,7 @@ process INDIVIDUAL_FINAL_ANALYSIS {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?")
END_VERSIONS
"""
}
6 changes: 3 additions & 3 deletions modules/local/silicolibrarygeneration/main.nf
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Expand Up @@ -3,8 +3,8 @@ process SILICOLIBRARYGENERATION {
label 'process_medium'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
'docker.io/biocontainers/diann:v1.8.1_cv1' }"
'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' :
'ghcr.io/bigbio/diann:1.9.1dev' }"

input:
file(fasta)
Expand Down Expand Up @@ -49,7 +49,7 @@ process SILICOLIBRARYGENERATION {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?")
END_VERSIONS
"""
}
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