From f2dc294f59d7c16b4c67cd4d8c24055e28a6a48d Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 13 Aug 2024 13:34:25 +0000 Subject: [PATCH 1/4] Update two modules --- modules.json | 4 ++-- modules/nf-core/kraken2/kraken2/tests/main.nf.test | 12 ++++++------ modules/nf-core/seqtk/sample/tests/main.nf.test | 6 +++--- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/modules.json b/modules.json index 07efcd04..2bf52fe9 100644 --- a/modules.json +++ b/modules.json @@ -57,7 +57,7 @@ }, "kraken2/kraken2": { "branch": "master", - "git_sha": "ca87ad032a62f025f0c373facacef2df0c5411b2", + "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc", "installed_by": ["fastq_contam_seqtk_kraken"] }, "md5sum": { @@ -72,7 +72,7 @@ }, "seqtk/sample": { "branch": "master", - "git_sha": "7f88aae93c69586c0789322b77743ee0ef469502", + "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", "installed_by": ["fastq_contam_seqtk_kraken"] }, "sgdemux": { diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test b/modules/nf-core/kraken2/kraken2/tests/main.nf.test index 4c513021..c0843df2 100644 --- a/modules/nf-core/kraken2/kraken2/tests/main.nf.test +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { input[0] = Channel.of([ [], file( - params.test_data['sarscov2']['genome']['kraken2_tar_gz'], + params.modules_testdata_base_path + "genomics/sarscov2/genome/db/kraken2.tar.gz", checkIfExists: true ) ]) @@ -32,7 +32,7 @@ nextflow_process { input[0] = [ [ id:'test', single_end:true ], // meta map [ file( - params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true )] ] @@ -69,16 +69,16 @@ nextflow_process { [ id:'test', single_end:false ], // meta map [ file( - params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true ), file( - params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true ) + ] ] - ] input[1] = UNTAR.out.untar.map{ it[1] } input[2] = true input[3] = false @@ -117,7 +117,7 @@ nextflow_process { input[0] = [ [ id:'test', single_end:true ], // meta map [ file( - params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true )] ] diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test b/modules/nf-core/seqtk/sample/tests/main.nf.test index 3063ea23..c121c9d9 100644 --- a/modules/nf-core/seqtk/sample/tests/main.nf.test +++ b/modules/nf-core/seqtk/sample/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), 50 ] """ @@ -39,7 +39,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), 50 ] """ @@ -62,7 +62,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), 50 ] """ From db045f0047d1410a9f01d7d3c8bc38867d31d493 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 13 Aug 2024 14:02:06 +0000 Subject: [PATCH 2/4] Bump to use nf-schema --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 61daeaf7..2cfb35f7 100755 --- a/nextflow.config +++ b/nextflow.config @@ -222,7 +222,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.0.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet } // Export these variables to prevent local Python/R libraries from conflicting with those in the container From 1136c7265422f2552d7c07c45bf963d30f03a4ec Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 13 Aug 2024 14:02:44 +0000 Subject: [PATCH 3/4] Use the latest version already --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 2cfb35f7..f0b2109e 100755 --- a/nextflow.config +++ b/nextflow.config @@ -222,7 +222,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-schema@2.0.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.0.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet } // Export these variables to prevent local Python/R libraries from conflicting with those in the container From 429188629b23f6777c64144b2f69740fe4700ec7 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 13 Aug 2024 14:11:37 +0000 Subject: [PATCH 4/4] Lets stay with nf-validation for now --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index f0b2109e..61daeaf7 100755 --- a/nextflow.config +++ b/nextflow.config @@ -222,7 +222,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-schema@2.0.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet } // Export these variables to prevent local Python/R libraries from conflicting with those in the container