From 39d52702aa7be35350233722875f45aa545f918c Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Fri, 31 May 2024 15:30:25 -0400 Subject: [PATCH 1/3] add tutorial --- assets/tutorial/airrflow.sh | 8 ++++++++ assets/tutorial/samplesheet.tsv | 6 ++++++ 2 files changed, 14 insertions(+) create mode 100644 assets/tutorial/airrflow.sh create mode 100644 assets/tutorial/samplesheet.tsv diff --git a/assets/tutorial/airrflow.sh b/assets/tutorial/airrflow.sh new file mode 100644 index 00000000..5f243b61 --- /dev/null +++ b/assets/tutorial/airrflow.sh @@ -0,0 +1,8 @@ +nextflow run nf-core/airrflow -r 4.1.0 \ +-profile docker \ +--mode assembled \ +--input samplesheet.tsv \ +--outdir results \ +-w work \ +--max_cpus 12 \ +--max_memory 12.GB diff --git a/assets/tutorial/samplesheet.tsv b/assets/tutorial/samplesheet.tsv new file mode 100644 index 00000000..69ca3c89 --- /dev/null +++ b/assets/tutorial/samplesheet.tsv @@ -0,0 +1,6 @@ +filename species subject_id sample_id day tissue sex age biomaterial_provider pcr_target_locus single_cell +https://zenodo.org/records/11373741/files/AIRR_subject1_FNA_d0_1_Y1.tsv human S1 S1_d0 d0 PMBC NA NA NA IG TRUE +https://zenodo.org/records/11373741/files/AIRR_subject1_FNA_d12_3_Y1.tsv human S1 S1_d12 d12 PMBC NA NA NA IG TRUE +https://zenodo.org/records/11373741/files/AIRR_subject2_FNA_d0_1_Y1.tsv human S2 S2_d0 d0 PMBC NA NA NA IG TRUE +https://zenodo.org/records/11373741/files/AIRR_subject2_FNA_d12_2_Y1.tsv human S2 S2_d12 d12 PMBC NA NA NA IG TRUE + From efda2c41aeeeef5238e7b8319b134c432949ad78 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Fri, 31 May 2024 15:30:34 -0400 Subject: [PATCH 2/3] simplify container --- modules/local/airrflow_report/airrflow_report.nf | 4 +--- modules/local/enchantr/collapse_duplicates.nf | 4 +--- modules/local/enchantr/define_clones.nf | 4 +--- modules/local/enchantr/detect_contamination.nf | 4 +--- modules/local/enchantr/dowser_lineages.nf | 4 +--- modules/local/enchantr/find_threshold.nf | 4 +--- modules/local/enchantr/remove_chimeric.nf | 4 +--- modules/local/enchantr/report_file_size.nf | 4 +--- modules/local/enchantr/single_cell_qc.nf | 4 +--- modules/local/enchantr/validate_input.nf | 4 +--- modules/local/reveal/add_meta_to_tab.nf | 4 +--- modules/local/reveal/filter_junction_mod3.nf | 4 +--- modules/local/reveal/filter_quality.nf | 4 +--- 13 files changed, 13 insertions(+), 39 deletions(-) diff --git a/modules/local/airrflow_report/airrflow_report.nf b/modules/local/airrflow_report/airrflow_report.nf index 243d2c75..990e492e 100644 --- a/modules/local/airrflow_report/airrflow_report.nf +++ b/modules/local/airrflow_report/airrflow_report.nf @@ -5,9 +5,7 @@ process AIRRFLOW_REPORT { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: tuple val(meta), path(tab) // sequence tsv table in AIRR format diff --git a/modules/local/enchantr/collapse_duplicates.nf b/modules/local/enchantr/collapse_duplicates.nf index 839af7b1..618491ab 100644 --- a/modules/local/enchantr/collapse_duplicates.nf +++ b/modules/local/enchantr/collapse_duplicates.nf @@ -7,9 +7,7 @@ process COLLAPSE_DUPLICATES { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: tuple val(meta), path(tabs) // tuple [val(meta), sequence tsv in AIRR format ] diff --git a/modules/local/enchantr/define_clones.nf b/modules/local/enchantr/define_clones.nf index 7efbc49c..ae71b900 100644 --- a/modules/local/enchantr/define_clones.nf +++ b/modules/local/enchantr/define_clones.nf @@ -24,9 +24,7 @@ process DEFINE_CLONES { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: tuple val(meta), path(tabs) // meta, sequence tsv in AIRR format diff --git a/modules/local/enchantr/detect_contamination.nf b/modules/local/enchantr/detect_contamination.nf index a7e5044c..cec4deca 100644 --- a/modules/local/enchantr/detect_contamination.nf +++ b/modules/local/enchantr/detect_contamination.nf @@ -8,9 +8,7 @@ process DETECT_CONTAMINATION { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: path(tabs) diff --git a/modules/local/enchantr/dowser_lineages.nf b/modules/local/enchantr/dowser_lineages.nf index 53f16ae2..0559c496 100644 --- a/modules/local/enchantr/dowser_lineages.nf +++ b/modules/local/enchantr/dowser_lineages.nf @@ -24,9 +24,7 @@ process DOWSER_LINEAGES { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: tuple val(meta), path(tabs) diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf index 8e741bea..4a9b0ab0 100644 --- a/modules/local/enchantr/find_threshold.nf +++ b/modules/local/enchantr/find_threshold.nf @@ -24,9 +24,7 @@ process FIND_THRESHOLD { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: diff --git a/modules/local/enchantr/remove_chimeric.nf b/modules/local/enchantr/remove_chimeric.nf index b8f9db1e..2df7e60c 100644 --- a/modules/local/enchantr/remove_chimeric.nf +++ b/modules/local/enchantr/remove_chimeric.nf @@ -8,9 +8,7 @@ process REMOVE_CHIMERIC { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: diff --git a/modules/local/enchantr/report_file_size.nf b/modules/local/enchantr/report_file_size.nf index fe7070ed..093a9e61 100644 --- a/modules/local/enchantr/report_file_size.nf +++ b/modules/local/enchantr/report_file_size.nf @@ -9,9 +9,7 @@ process REPORT_FILE_SIZE { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: path logs diff --git a/modules/local/enchantr/single_cell_qc.nf b/modules/local/enchantr/single_cell_qc.nf index c330d1e3..4170e51b 100644 --- a/modules/local/enchantr/single_cell_qc.nf +++ b/modules/local/enchantr/single_cell_qc.nf @@ -23,9 +23,7 @@ process SINGLE_CELL_QC { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: path(tabs) diff --git a/modules/local/enchantr/validate_input.nf b/modules/local/enchantr/validate_input.nf index 278184f3..6ec12543 100644 --- a/modules/local/enchantr/validate_input.nf +++ b/modules/local/enchantr/validate_input.nf @@ -9,9 +9,7 @@ process VALIDATE_INPUT { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: file samplesheet diff --git a/modules/local/reveal/add_meta_to_tab.nf b/modules/local/reveal/add_meta_to_tab.nf index a46b9e3f..1c50d60e 100644 --- a/modules/local/reveal/add_meta_to_tab.nf +++ b/modules/local/reveal/add_meta_to_tab.nf @@ -6,9 +6,7 @@ process ADD_META_TO_TAB { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" cache 'deep' // Without 'deep' this process would run when using -resume diff --git a/modules/local/reveal/filter_junction_mod3.nf b/modules/local/reveal/filter_junction_mod3.nf index ba4484b2..92ef4833 100644 --- a/modules/local/reveal/filter_junction_mod3.nf +++ b/modules/local/reveal/filter_junction_mod3.nf @@ -6,9 +6,7 @@ process FILTER_JUNCTION_MOD3 { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: tuple val(meta), path(tab) // sequence tsv in AIRR format diff --git a/modules/local/reveal/filter_quality.nf b/modules/local/reveal/filter_quality.nf index a08472e7..4675ed17 100644 --- a/modules/local/reveal/filter_quality.nf +++ b/modules/local/reveal/filter_quality.nf @@ -6,9 +6,7 @@ process FILTER_QUALITY { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:4.1.0': - 'docker.io/immcantation/airrflow:4.1.0' }" + container "docker.io/immcantation/airrflow:4.1.0" input: tuple val(meta), path(tab) // sequence tsv in AIRR format From 0d30d4c6768d54bed95c3324516a11941b0320d6 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Fri, 31 May 2024 15:34:57 -0400 Subject: [PATCH 3/3] update test data param --- conf/test.config | 10 +++++----- conf/test_10x_sc.config | 4 ++-- conf/test_assembled_hs.config | 6 +++--- conf/test_assembled_immcantation_devel_hs.config | 6 +++--- conf/test_assembled_immcantation_devel_mm.config | 6 +++--- conf/test_assembled_mm.config | 6 +++--- conf/test_clontech_umi.config | 6 +++--- conf/test_fetchimgt.config | 6 +++--- conf/test_full.config | 6 +++--- conf/test_nebnext_umi.config | 6 +++--- conf/test_no_umi.config | 10 +++++----- conf/test_nocluster.config | 10 +++++----- conf/test_raw_immcantation_devel.config | 10 +++++----- conf/test_tcr.config | 10 +++++----- nextflow.config | 2 +- 15 files changed, 52 insertions(+), 52 deletions(-) diff --git a/conf/test.config b/conf/test.config index b9b0b19a..af9618ce 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,11 +20,11 @@ params { max_time = '6.h' // Input data - input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv' - cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta' - vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv' + cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta' + vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' mode = 'fastq' diff --git a/conf/test_10x_sc.config b/conf/test_10x_sc.config index 4eb926b4..e9b9e5a8 100644 --- a/conf/test_10x_sc.config +++ b/conf/test_10x_sc.config @@ -23,6 +23,6 @@ params { // Input data - input = pipelines_testdata_base_path + 'airrflow/testdata-sc/10x_sc_raw.tsv' - reference_10x = pipelines_testdata_base_path + 'airrflow/testdata-sc/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz' + input = pipelines_testdata_base_path + 'testdata-sc/10x_sc_raw.tsv' + reference_10x = pipelines_testdata_base_path + 'testdata-sc/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz' } diff --git a/conf/test_assembled_hs.config b/conf/test_assembled_hs.config index e8f1462c..9e3d7f5b 100644 --- a/conf/test_assembled_hs.config +++ b/conf/test_assembled_hs.config @@ -18,9 +18,9 @@ params { // Input data mode = 'assembled' - input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_hs.tsv' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' reassign = true productive_only = true diff --git a/conf/test_assembled_immcantation_devel_hs.config b/conf/test_assembled_immcantation_devel_hs.config index adc0332b..c842e002 100644 --- a/conf/test_assembled_immcantation_devel_hs.config +++ b/conf/test_assembled_immcantation_devel_hs.config @@ -18,9 +18,9 @@ params { // Input data mode = 'assembled' - input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_hs.tsv' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' reassign = true productive_only = true diff --git a/conf/test_assembled_immcantation_devel_mm.config b/conf/test_assembled_immcantation_devel_mm.config index 3bc602ea..e148abe8 100644 --- a/conf/test_assembled_immcantation_devel_mm.config +++ b/conf/test_assembled_immcantation_devel_mm.config @@ -18,9 +18,9 @@ params { // Input data mode = 'assembled' - input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_mm.tsv' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_mm.tsv' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' reassign = true productive_only = true diff --git a/conf/test_assembled_mm.config b/conf/test_assembled_mm.config index f90e7319..43e8275e 100644 --- a/conf/test_assembled_mm.config +++ b/conf/test_assembled_mm.config @@ -18,9 +18,9 @@ params { // Input data mode = 'assembled' - input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_mm.tsv' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_mm.tsv' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' reassign = true productive_only = true diff --git a/conf/test_clontech_umi.config b/conf/test_clontech_umi.config index 55dda02a..e1bf317e 100644 --- a/conf/test_clontech_umi.config +++ b/conf/test_clontech_umi.config @@ -21,10 +21,10 @@ params { max_time = '6.h' // Input data - input = pipelines_testdata_base_path +'airrflow/testdata-clontech/samplesheet.tsv' + input = pipelines_testdata_base_path +'testdata-clontech/samplesheet.tsv' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' clonal_threshold = 0.1 diff --git a/conf/test_fetchimgt.config b/conf/test_fetchimgt.config index 14431d1b..468bb52d 100644 --- a/conf/test_fetchimgt.config +++ b/conf/test_fetchimgt.config @@ -20,9 +20,9 @@ params { max_time = '6.h' // Input data - input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv' - cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta' - vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta' + input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv' + cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta' + vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta' fetch_imgt = true mode = 'fastq' diff --git a/conf/test_full.config b/conf/test_full.config index f6146bcf..9c652c8f 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,11 +15,11 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data - input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/metadata_pcr_umi_airr_300.tsv' + input = pipelines_testdata_base_path + 'testdata-bcr/metadata_pcr_umi_airr_300.tsv' cprimers = 's3://ngi-igenomes/test-data/airrflow/pcr_umi/cprimers.fasta' vprimers = 's3://ngi-igenomes/test-data/airrflow/pcr_umi/vprimers.fasta' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' lineage_trees = true diff --git a/conf/test_nebnext_umi.config b/conf/test_nebnext_umi.config index ff7c22d8..b26fa7cd 100644 --- a/conf/test_nebnext_umi.config +++ b/conf/test_nebnext_umi.config @@ -22,10 +22,10 @@ params { max_time = '6.h' // Input data - input = pipelines_testdata_base_path + 'airrflow/testdata-neb/samplesheet.tsv' + input = pipelines_testdata_base_path + 'testdata-neb/samplesheet.tsv' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' clonal_threshold = 0.1 diff --git a/conf/test_no_umi.config b/conf/test_no_umi.config index b694e796..3a4fad63 100644 --- a/conf/test_no_umi.config +++ b/conf/test_no_umi.config @@ -27,11 +27,11 @@ params { isotype_column = 'c_primer' // Input data - input = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Metadata_test-no-umi_airr.tsv' - cprimers = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Greiff2014_CPrimers.fasta' - vprimers = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Greiff2014_VPrimers.fasta' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'testdata-no-umi/Metadata_test-no-umi_airr.tsv' + cprimers = pipelines_testdata_base_path + 'testdata-no-umi/Greiff2014_CPrimers.fasta' + vprimers = pipelines_testdata_base_path + 'testdata-no-umi/Greiff2014_VPrimers.fasta' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' } diff --git a/conf/test_nocluster.config b/conf/test_nocluster.config index c1b3d10b..4a3fb0b7 100644 --- a/conf/test_nocluster.config +++ b/conf/test_nocluster.config @@ -20,11 +20,11 @@ params { max_time = '6.h' // Input data - input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv' - cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta' - vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv' + cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta' + vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' mode = 'fastq' diff --git a/conf/test_raw_immcantation_devel.config b/conf/test_raw_immcantation_devel.config index a897d1ce..567629a9 100644 --- a/conf/test_raw_immcantation_devel.config +++ b/conf/test_raw_immcantation_devel.config @@ -20,12 +20,12 @@ params { max_time = '6.h' // Input data - input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv' - cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta' - vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta' + input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv' + cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta' + vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' mode = 'fastq' diff --git a/conf/test_tcr.config b/conf/test_tcr.config index a178ba5d..7572f099 100644 --- a/conf/test_tcr.config +++ b/conf/test_tcr.config @@ -28,11 +28,11 @@ params { // Input data - input = pipelines_testdata_base_path + 'airrflow/testdata-tcr/TCR_metadata_airr.tsv' - cprimers = pipelines_testdata_base_path + 'airrflow/testdata-tcr/cprimers.fasta' - race_linker = pipelines_testdata_base_path + 'airrflow/testdata-tcr/linker.fasta' - reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' - reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'testdata-tcr/TCR_metadata_airr.tsv' + cprimers = pipelines_testdata_base_path + 'testdata-tcr/cprimers.fasta' + race_linker = pipelines_testdata_base_path + 'testdata-tcr/linker.fasta' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' } diff --git a/nextflow.config b/nextflow.config index 3dfaec00..948a35ff 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,7 +14,7 @@ params { mode = "fastq" miairr="$projectDir/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsv" index_file = false - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/' // ---------------------------- // sequencing protocol options