From b57961abf76589ee586e82eb3287ac1b0318124a Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Mon, 1 Jul 2024 18:38:57 +0100 Subject: [PATCH 1/5] diann 1.8.1 -> 1.9.1dev --- modules/local/assemble_empirical_library/main.nf | 4 ++-- modules/local/diann_preliminary_analysis/main.nf | 4 ++-- modules/local/diannsummary/main.nf | 4 ++-- modules/local/individual_final_analysis/main.nf | 4 ++-- modules/local/silicolibrarygeneration/main.nf | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/modules/local/assemble_empirical_library/main.nf b/modules/local/assemble_empirical_library/main.nf index 14eb19e2..b5b36ce5 100644 --- a/modules/local/assemble_empirical_library/main.nf +++ b/modules/local/assemble_empirical_library/main.nf @@ -3,8 +3,8 @@ process ASSEMBLE_EMPIRICAL_LIBRARY { label 'process_low' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' : - 'docker.io/biocontainers/diann:v1.8.1_cv1' }" + 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' : + 'ghcr.io/bigbio/diann:1.9.1dev' }" input: // In this step the real files are passed, and not the names diff --git a/modules/local/diann_preliminary_analysis/main.nf b/modules/local/diann_preliminary_analysis/main.nf index fe995ece..c57937de 100644 --- a/modules/local/diann_preliminary_analysis/main.nf +++ b/modules/local/diann_preliminary_analysis/main.nf @@ -3,8 +3,8 @@ process DIANN_PRELIMINARY_ANALYSIS { label 'process_high' container "${ 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) diff --git a/modules/local/diannsummary/main.nf b/modules/local/diannsummary/main.nf index 4677b3e3..32dc2e44 100644 --- a/modules/local/diannsummary/main.nf +++ b/modules/local/diannsummary/main.nf @@ -3,8 +3,8 @@ process DIANNSUMMARY { label 'process_high' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' : - 'docker.io/biocontainers/diann:v1.8.1_cv1' }" + 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' : + 'ghcr.io/bigbio/diann:1.9.1dev' }" input: // Note that the files are passed as names and not paths, this prevents them from being staged diff --git a/modules/local/individual_final_analysis/main.nf b/modules/local/individual_final_analysis/main.nf index f80b047a..ddc9221e 100644 --- a/modules/local/individual_final_analysis/main.nf +++ b/modules/local/individual_final_analysis/main.nf @@ -3,8 +3,8 @@ process INDIVIDUAL_FINAL_ANALYSIS { label 'process_high' container "${ 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) diff --git a/modules/local/silicolibrarygeneration/main.nf b/modules/local/silicolibrarygeneration/main.nf index e5f6e2f3..99482403 100644 --- a/modules/local/silicolibrarygeneration/main.nf +++ b/modules/local/silicolibrarygeneration/main.nf @@ -3,8 +3,8 @@ process SILICOLIBRARYGENERATION { label 'process_medium' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' : - 'docker.io/biocontainers/diann:v1.8.1_cv1' }" + 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' : + 'ghcr.io/bigbio/diann:1.9.1dev' }" input: file(fasta) From 766ffc33601dc5e2094f59627cc5b659b70ec7be Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 2 Jul 2024 11:06:28 +0100 Subject: [PATCH 2/5] diann 1.8.1 -> 1.9.1dev --- modules/local/diann_preliminary_analysis/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/diann_preliminary_analysis/main.nf b/modules/local/diann_preliminary_analysis/main.nf index c57937de..e5401c2c 100644 --- a/modules/local/diann_preliminary_analysis/main.nf +++ b/modules/local/diann_preliminary_analysis/main.nf @@ -61,7 +61,7 @@ process DIANN_PRELIMINARY_ANALYSIS { cat <<-END_VERSIONS > versions.yml "${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 """ } From 6317c6b814bc9ef54f7f8d60fab21c067ec5517d Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 2 Jul 2024 11:15:20 +0100 Subject: [PATCH 3/5] diann 1.8.1 -> 1.9.1dev --- modules/local/assemble_empirical_library/main.nf | 2 +- modules/local/diannsummary/main.nf | 2 +- modules/local/individual_final_analysis/main.nf | 2 +- modules/local/silicolibrarygeneration/main.nf | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/local/assemble_empirical_library/main.nf b/modules/local/assemble_empirical_library/main.nf index b5b36ce5..853925c2 100644 --- a/modules/local/assemble_empirical_library/main.nf +++ b/modules/local/assemble_empirical_library/main.nf @@ -58,7 +58,7 @@ process ASSEMBLE_EMPIRICAL_LIBRARY { cat <<-END_VERSIONS > versions.yml "${task.process}": - DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)") + DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?") END_VERSIONS """ } diff --git a/modules/local/diannsummary/main.nf b/modules/local/diannsummary/main.nf index 32dc2e44..86c9d132 100644 --- a/modules/local/diannsummary/main.nf +++ b/modules/local/diannsummary/main.nf @@ -69,7 +69,7 @@ process DIANNSUMMARY { cat <<-END_VERSIONS > versions.yml "${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 """ } diff --git a/modules/local/individual_final_analysis/main.nf b/modules/local/individual_final_analysis/main.nf index ddc9221e..21c0d375 100644 --- a/modules/local/individual_final_analysis/main.nf +++ b/modules/local/individual_final_analysis/main.nf @@ -53,7 +53,7 @@ process INDIVIDUAL_FINAL_ANALYSIS { cat <<-END_VERSIONS > versions.yml "${task.process}": - DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)") + DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?") END_VERSIONS """ } diff --git a/modules/local/silicolibrarygeneration/main.nf b/modules/local/silicolibrarygeneration/main.nf index 99482403..55169a7b 100644 --- a/modules/local/silicolibrarygeneration/main.nf +++ b/modules/local/silicolibrarygeneration/main.nf @@ -49,7 +49,7 @@ process SILICOLIBRARYGENERATION { cat <<-END_VERSIONS > versions.yml "${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 """ } From 9cb39228d51f6758aa28f98594608e316de1f5cc Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 2 Jul 2024 11:46:40 +0100 Subject: [PATCH 4/5] diann 1.8.1 -> 1.9.1dev --- modules/local/diannsummary/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/local/diannsummary/main.nf b/modules/local/diannsummary/main.nf index 86c9d132..70b707c1 100644 --- a/modules/local/diannsummary/main.nf +++ b/modules/local/diannsummary/main.nf @@ -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: From 96d1d1c446d9aa71ee02dde3e10a45fb217ffd12 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 2 Jul 2024 12:11:50 +0100 Subject: [PATCH 5/5] diann 1.8.1 -> 1.9.1dev --- bin/diann_convert.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/diann_convert.py b/bin/diann_convert.py index fb2bdd22..f385b607 100755 --- a/bin/diann_convert.py +++ b/bin/diann_convert.py @@ -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}")