From e74b2f34a44b428a457d90f78a12cdea4889259c Mon Sep 17 00:00:00 2001 From: MUSKAN <615muskanyadav@gmail.com> Date: Thu, 12 Mar 2026 17:30:47 +0530 Subject: [PATCH 1/5] Create meta.yml This PR adds the missing meta.yml and nf-test for functional annotation as a part of March 2025 Hackathon. --- .../local/functional_annotation/meta.yml | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 subworkflows/local/functional_annotation/meta.yml diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml new file mode 100644 index 0000000..0eeefa1 --- /dev/null +++ b/subworkflows/local/functional_annotation/meta.yml @@ -0,0 +1,62 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "functional_annotation" +description: Perform local functional annotation on protien sequences +keywords: + - fasta + - sequences + - functional + - domain + - annotation + - database + - download + - HMM +components: + - aria2 + - hmmer/hmmsearch +input: + - ch_fasta: + type: file + description: | + Amino acid fasta file containing amino acid sequences for annotation + Structure: [ val(meta), [ path(fasta) ] ] + - skip_pfam: + type: boolean + description: | + Skip domain annotation with Pfam + - pfam_db: + type: string + description: | + Path to an existing HMM Pfam library on the system. If provided, the ARIA2_PFAM db download will be skipped. + - pfam_latest_link: + type: string + description: | + Path to the latest Pfam HMM database, to download + - skip_funfam: + type: boolean + description: | + Skip domain annotation with FunFam + - funfam_db: + type: string + description: | + Path to an existing HMM FunFam library on the system. If provided, the ARIA2_FUNFAM db download will be skipped. + - funfam_latest_link: + type: string + description: | + Path to the latest FunFam HMM database, to download +output: + - pfam_domains: + type: file + description: | + domtbl.gz files with pfam domain annotation for input amino acid sequences + - funfam_domains: + type: file + description: | + domtbl.gz files with funfam domain annotation for input amino acid sequences + - versions: + type: file + description: | + Versions file containing the software versions used in the workflow +authors: + - "@vagkaratzas" +maintainers: + - "@vagkaratzas" From 0e9b00032ebe2985f6636b5b46e2714fc6be8f4f Mon Sep 17 00:00:00 2001 From: MUSKAN <615muskanyadav@gmail.com> Date: Thu, 12 Mar 2026 18:06:09 +0530 Subject: [PATCH 2/5] meta.yml added meta.yml file --- subworkflows/local/functional_annotation/meta.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml index 0eeefa1..1b063e1 100644 --- a/subworkflows/local/functional_annotation/meta.yml +++ b/subworkflows/local/functional_annotation/meta.yml @@ -58,5 +58,6 @@ output: Versions file containing the software versions used in the workflow authors: - "@vagkaratzas" + - "@Muskan-2464" maintainers: - "@vagkaratzas" From 340d27bf22bd7f1558bd1025c8b50625dec1d8d0 Mon Sep 17 00:00:00 2001 From: MUSKAN <615muskanyadav@gmail.com> Date: Thu, 12 Mar 2026 18:25:45 +0530 Subject: [PATCH 3/5] Create nf test nf test 21 --- tests/nf test | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 tests/nf test diff --git a/tests/nf test b/tests/nf test new file mode 100644 index 0000000..0174de9 --- /dev/null +++ b/tests/nf test @@ -0,0 +1,33 @@ +nextflow_workflow { + + name "Test Subworkflow functional_annotation" + script "../main.nf" + workflow "functional_annotation" + + test("Should run functional annotation successfully") { + + when { + workflow { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + input[1] = false // skip_pfam + input[2] = [] // pfam_db + input[3] = "https://raw.githubusercontent.com/nf-core/test-datasets/multiqc/testdata/set_indices.txt" + input[4] = true // skip_funfam + input[5] = [] // funfam_db + input[6] = [] // funfam_latest_link + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} From a00141d2185a93eb9f686e94f6e0ad47c5900af4 Mon Sep 17 00:00:00 2001 From: MUSKAN <615muskanyadav@gmail.com> Date: Thu, 12 Mar 2026 18:32:55 +0530 Subject: [PATCH 4/5] meta.yml6 --- subworkflows/local/functional_annotation/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml index 1b063e1..831e917 100644 --- a/subworkflows/local/functional_annotation/meta.yml +++ b/subworkflows/local/functional_annotation/meta.yml @@ -1,5 +1,5 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "functional_annotation" +name: "FUNCTIIONAL_ANNOTATIONS" description: Perform local functional annotation on protien sequences keywords: - fasta From 2717a6115365fab6256e736896de4ce7a4132b7e Mon Sep 17 00:00:00 2001 From: MUSKAN <615muskanyadav@gmail.com> Date: Thu, 12 Mar 2026 18:34:12 +0530 Subject: [PATCH 5/5] nf test --- tests/nf test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/nf test b/tests/nf test index 0174de9..7547264 100644 --- a/tests/nf test +++ b/tests/nf test @@ -2,7 +2,7 @@ nextflow_workflow { name "Test Subworkflow functional_annotation" script "../main.nf" - workflow "functional_annotation" + workflow "FUNCTIIONAL_ANNOTATIONS" test("Should run functional annotation successfully") {