fix issues template update

ggabernet · Oct 14, 2024 · 8fd8a04 · 8fd8a04
1 parent 1461dd3
commit 8fd8a04
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Showing 21 changed files with 26 additions and 104 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#344](https://github.com/nf-core/airrflow/pull/344) Added option to remove V and C primer region when sequence is unknown.
 - [#344](https://github.com/nf-core/airrflow/pull/344) Added option to save non-productive sequences
 - [#344](https://github.com/nf-core/airrflow/pull/344) Allow for maskprimers align with UMI on both V gene and C gene primers.
+- [#344](https://github.com/nf-core/airrflow/pull/344) Update pipeline template to nf-core tools v3.0.2.
 
 ### `Fixed`
 

diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -48,6 +48,26 @@
                 "type": "boolean",
                 "pattern": "^\\S+$",
                 "errorMessage": "Single cell must be provided as a TRUE/FALSE value."
+            },
+            "filename_R1": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Filename for R1 cannot contain spaces."
+            },
+            "filename_R2": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Filename for R2 cannot contain spaces."
+            },
+            "filename_I1": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Filename for I1 cannot contain spaces."
+            },
+            "filename": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Filename cannot contain spaces."
             }
         },
         "required": [

diff --git a/assets/tutorial/airrflow.sh b/assets/tutorial/airrflow.sh
@@ -4,6 +4,4 @@ nextflow run nf-core/airrflow -r 4.1.0 \
 --input samplesheet.tsv \
 --outdir results \
 -w work \
---max_cpus 12 \
---max_memory 12.GB \
 --skip_multiqc
diff --git a/conf/base.config b/conf/base.config
@@ -58,8 +58,8 @@ process {
         maxRetries    = 2
     }
     withLabel:process_long_parallelized {
-        time   = { 30.h  * task.attempt, 'time'  }
-        cpus   = { 16    * task.attempt, 'cpus'  }
-        memory = { 72.GB * task.attempt, 'memory'}
+        time   = { 30.h  * task.attempt }
+        cpus   = { 16    * task.attempt }
+        memory = { 72.GB * task.attempt }
     }
 }
diff --git a/conf/test_10x_sc.config b/conf/test_10x_sc.config
@@ -19,11 +19,6 @@ params {
     config_profile_name = 'Test 10xGenomics single cell data'
     config_profile_description = 'Minimal test dataset to check pipeline function with raw single cell data from 10xGenomics'
 
-    // 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 = 'sc_10x_genomics'

diff --git a/conf/test_assembled_hs.config b/conf/test_assembled_hs.config
@@ -19,11 +19,6 @@ params {
     config_profile_name        = 'Test assembled mode'
     config_profile_description = 'Minimal test dataset to test assembled mode'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     mode = 'assembled'
     input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv'

diff --git a/conf/test_assembled_immcantation_devel_hs.config b/conf/test_assembled_immcantation_devel_hs.config
@@ -19,11 +19,6 @@ params {
     config_profile_name        = 'Test assembled mode with Immcantation custom_container'
     config_profile_description = 'Minimal human test dataset to check pipeline function on assembled mode with Immcantation custom_container'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     mode = 'assembled'
     input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv'

diff --git a/conf/test_assembled_immcantation_devel_mm.config b/conf/test_assembled_immcantation_devel_mm.config
@@ -19,11 +19,6 @@ params {
     config_profile_name        = 'Test assembled mode with Immcantation custom_container'
     config_profile_description = 'Minimal mouse test dataset to check pipeline function on assembled mode with Immcantation custom_container'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     mode = 'assembled'
     input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_mm.tsv'

diff --git a/conf/test_assembled_mm.config b/conf/test_assembled_mm.config
@@ -19,11 +19,6 @@ params {
     config_profile_name        = 'Test assembled mode'
     config_profile_description = 'Minimal mouse test dataset to test assembled mode'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     mode = 'assembled'
     input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_mm.tsv'

diff --git a/conf/test_clontech_umi.config b/conf/test_clontech_umi.config
@@ -23,11 +23,6 @@ params {
     config_profile_name        = 'Test profile for TAKARA protocol'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input = pipelines_testdata_base_path +'testdata-clontech/samplesheet.tsv'
 

diff --git a/conf/test_fetchimgt.config b/conf/test_fetchimgt.config
@@ -21,11 +21,6 @@ params {
     config_profile_name        = 'Test IMGTdb fetch'
     config_profile_description = 'Test pipeline when fetching the latest version of the IMGT references.'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv'
     cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'

diff --git a/conf/test_maskprimers_align.config b/conf/test_maskprimers_align.config
@@ -21,11 +21,6 @@ params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv'
     cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'

diff --git a/conf/test_maskprimers_extract.config b/conf/test_maskprimers_extract.config
@@ -21,11 +21,6 @@ params {
     config_profile_name        = 'Test extract primers profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv'
     reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'

diff --git a/conf/test_nebnext_umi.config b/conf/test_nebnext_umi.config
@@ -24,11 +24,6 @@ params {
     config_profile_name        = 'Test profile for NEBNext protocol'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input = pipelines_testdata_base_path + 'testdata-neb/samplesheet.tsv'
 

diff --git a/conf/test_no_umi.config b/conf/test_no_umi.config
@@ -18,11 +18,6 @@ params {
     config_profile_name = 'Test profile without UMIs'
     config_profile_description = 'Test dataset without UMIs to check pipeline function.'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus = 2
-    max_memory = 6.GB
-    max_time = 6.h
-
     mode = 'fastq'
 
     cprimer_position = 'R1'

diff --git a/conf/test_nocluster.config b/conf/test_nocluster.config
@@ -21,11 +21,6 @@ params {
     config_profile_name        = 'Test profile no cluster sets'
     config_profile_description = 'Test pipeline without the cluster sets process'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv'
     cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'

diff --git a/conf/test_raw_immcantation_devel.config b/conf/test_raw_immcantation_devel.config
@@ -21,11 +21,6 @@ params {
     config_profile_name        = 'Test immcantation raw profile'
     config_profile_description = 'Minimal test dataset to check pipeline function with the immcantation container'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv'
     cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'

diff --git a/conf/test_rnaseq_bulk.config b/conf/test_rnaseq_bulk.config
@@ -18,11 +18,6 @@ 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'

diff --git a/conf/test_rnaseq_sc.config b/conf/test_rnaseq_sc.config
@@ -18,11 +18,6 @@ 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'

diff --git a/conf/test_tcr.config b/conf/test_tcr.config
@@ -19,11 +19,6 @@ params {
     config_profile_name = 'Test TCR'
     config_profile_description = 'Minimal test dataset to check pipeline function with TCR 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'
     umi_length = 12

diff --git a/subworkflows/local/utils_nfcore_airrflow_pipeline/main.nf b/subworkflows/local/utils_nfcore_airrflow_pipeline/main.nf
@@ -71,26 +71,9 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
+    Channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
 
-    Channel
-        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
-        .map {
-            meta, fastq_1, fastq_2 ->
-                if (!fastq_2) {
-                    return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
-                } else {
-                    return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
-                }
-        }
-        .groupTuple()
-        .map { samplesheet ->
-            validateInputSamplesheet(samplesheet)
-        }
-        .map {
-            meta, fastqs ->
-                return [ meta, fastqs.flatten() ]
-        }
-        .set { ch_samplesheet }
+    Channel.fromPath(input).set{ch_samplesheet}
 
     emit:
     samplesheet = ch_samplesheet