nf-core · ggabernet · Jul 17, 2024 · Mar 21, 2024 · Mar 25, 2024 · Apr 10, 2024
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -62,6 +62,8 @@ jobs:
             "test_10x_sc",
             "test_clontech_umi",
             "test_nebnext_umi",
+            "test_rnaseq_bulk",
+            "test_rnaseq_sc",
           ]
       fail-fast: false
     steps:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
 | biopython  | 1.71        | 1.81        |
+| enchantr   | 0.1.15      | 0.1.16      |
+| scoper     | 1.2.1       | 1.3.0       |
+| dowser     | 1.2.0       | 2.1.0       |
+| igphyml    | 1.1.5       | 2.0.0       |
 
 ## [4.0] - 2024-04-22 Ascendio
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -422,6 +422,14 @@ process {
         ]
     }
 
+    withName: CHANGEO_PARSEDB_SELECT_LOCUS {
+        publishDir = [
+            path: { "${params.outdir}/vdj_annotation/select-locus/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: CHANGEO_PARSEDB_SPLIT {
         publishDir = [
             path: { "${params.outdir}/vdj_annotation/04-select-productive/${meta.id}" },

diff --git a/conf/test_rnaseq_bulk.config b/conf/test_rnaseq_bulk.config
@@ -0,0 +1,26 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/airrflow -profile test_rnaseq_bulk,<docker/singularity>
+ */
+
+params {
+    config_profile_name = 'Test bulk RNA-seq based workflow using TRUST4'
+    config_profile_description = 'Minimal test dataset to check pipeline function with raw bulk RNA-seq data'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus = 2
+    max_memory = 6.GB
+    max_time = 48.h
+
+    // params
+    mode = 'fastq'
+    library_generation_method = 'trust4'
+    clonal_threshold = 0
+
+    // Input data
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-rnaseq/rnaseq_metadata.tsv'
+}
diff --git a/conf/test_rnaseq_sc.config b/conf/test_rnaseq_sc.config
@@ -0,0 +1,30 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/airrflow -profile test_rnaseq_sc,<docker/singularity>
+ */
+
+params {
+    config_profile_name = 'Test single-cell RNA-seq based workflow using TRUST4'
+    config_profile_description = 'Minimal test dataset to check pipeline function with raw single-cell RNA-seq data'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus = 2
+    max_memory = 6.GB
+    max_time = 48.h
+
+    // params
+    mode = 'fastq'
+    library_generation_method = 'trust4'
+    clonal_threshold = 0
+    barcode_read = "R1"
+    umi_read = "R1"
+    read_format = "bc:0:15,um:16:27"
+    skip_lineage = true
+
+    // Input data
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-rnaseq/sc_rnaseq_metadata.tsv'
+}
diff --git a/docs/usage.md b/docs/usage.md
diff --git a/modules.json b/modules.json
@@ -34,6 +34,11 @@
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
+                    },
+                    "trust4": {
+                        "branch": "master",
+                        "git_sha": "bbb9636dbe460f45fe786d0866f8fd7337e4fc7a",
+                        "installed_by": ["modules"]
                     }
                 }
             },

diff --git a/modules/local/airrflow_report/airrflow_report.nf b/modules/local/airrflow_report/airrflow_report.nf
@@ -6,8 +6,8 @@ process AIRRFLOW_REPORT {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        'docker.io/immcantation/airrflow:4.1.0' }"
 
     input:
     tuple val(meta), path(tab) // sequence tsv table in AIRR format

diff --git a/...s/local/changeo/changeo_parsedb_select.nf → ...l/changeo/changeo_parsedb_select_locus.nf b/...s/local/changeo/changeo_parsedb_select.nf → ...l/changeo/changeo_parsedb_select_locus.nf
@@ -1,4 +1,4 @@
-process CHANGEO_PARSEDB_SELECT {
+process CHANGEO_PARSEDB_SELECT_LOCUS {
     tag "$meta.id"
     label 'process_low'
     label 'immcantation'
@@ -18,25 +18,21 @@ process CHANGEO_PARSEDB_SELECT {
     path "versions.yml" , emit: versions
 
     script:
-    def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
     if (meta.locus.toUpperCase() == 'IG'){
         """
-        ParseDb.py select -d $tab $args --outname ${meta.id} > ${meta.id}_select_command_log.txt
+        ParseDb.py select -d $tab -f locus -u "IG[HKL]" --regex --outname ${meta.id} > ${meta.id}_select_command_log.txt
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            igblastn: \$( igblastn -version | grep -o "igblast[0-9\\. ]\\+" | grep -o "[0-9\\. ]\\+" )
             changeo: \$( ParseDb.py --version | awk -F' '  '{print \$2}' )
         END_VERSIONS
         """
     } else if (meta.locus.toUpperCase() == 'TR'){
         """
-        ParseDb.py select -d $tab $args2 --outname ${meta.id} > "${meta.id}_command_log.txt"
+        ParseDb.py select -d $tab -f locus -u "TR[ABDG]" --regex --outname ${meta.id} > "${meta.id}_command_log.txt"
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            igblastn: \$( igblastn -version | grep -o "igblast[0-9\\. ]\\+" | grep -o "[0-9\\. ]\\+" )
             changeo: \$( ParseDb.py --version | awk -F' '  '{print \$2}' )
         END_VERSIONS
         """

diff --git a/modules/local/enchantr/collapse_duplicates.nf b/modules/local/enchantr/collapse_duplicates.nf
@@ -8,8 +8,8 @@ process COLLAPSE_DUPLICATES {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        '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
@@ -25,8 +25,8 @@ process DEFINE_CLONES {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        '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
@@ -9,8 +9,8 @@ process DETECT_CONTAMINATION {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        '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
@@ -25,8 +25,8 @@ process DOWSER_LINEAGES {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        '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
@@ -25,8 +25,8 @@ process FIND_THRESHOLD {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        'docker.io/immcantation/airrflow:4.1.0' }"
 
 
     input:

diff --git a/modules/local/enchantr/remove_chimeric.nf b/modules/local/enchantr/remove_chimeric.nf
@@ -9,8 +9,8 @@ process REMOVE_CHIMERIC {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        '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
@@ -10,8 +10,8 @@ process REPORT_FILE_SIZE {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        '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
@@ -24,8 +24,8 @@ process SINGLE_CELL_QC {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        '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
@@ -10,8 +10,8 @@ process VALIDATE_INPUT {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        'docker.io/immcantation/airrflow:4.1.0' }"
 
     input:
     file samplesheet

diff --git a/modules/local/prepare_trust4_reference.nf b/modules/local/prepare_trust4_reference.nf
@@ -0,0 +1,24 @@
+process PREPARE_TRUST4_REFERENCE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::trust4=1.0.13"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/trust4:1.0.13--h43eeafb_0':
+        'biocontainers/trust4:1.0.13--h43eeafb_0' }"
+
+    input:
+    tuple val(meta), path(R1), path(R2)
+    path(reference_igblast)
+
+    output:
+    tuple val(meta), path("trust4_reference.fa") , emit: trust4_reference
+
+    script:
+    """
+    cat ${reference_igblast}/fasta/imgt_${meta.species.toLowerCase()}_*.fasta \\
+    ${reference_igblast}/fasta/imgt_${meta.species.toLowerCase()}_*.fasta >> trust4_reference.fa
+    """
+
+
+}
diff --git a/modules/local/reveal/add_meta_to_tab.nf b/modules/local/reveal/add_meta_to_tab.nf
@@ -7,8 +7,8 @@ process ADD_META_TO_TAB {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        '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
@@ -7,8 +7,8 @@ process FILTER_JUNCTION_MOD3 {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        '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
@@ -7,8 +7,8 @@ process FILTER_QUALITY {
         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:4.0.0':
-        'docker.io/immcantation/airrflow:4.0.0' }"
+        'docker.io/immcantation/airrflow:4.1.0':
+        'docker.io/immcantation/airrflow:4.1.0' }"
 
     input:
     tuple val(meta), path(tab) // sequence tsv in AIRR format

diff --git a/modules/nf-core/trust4/environment.yml b/modules/nf-core/trust4/environment.yml