From 17fe1fd5e603d52c1c5f56ac4cab7b0ba0742791 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 13 Apr 2020 21:06:45 -0500
Subject: [PATCH] Revert to layered configs

---
 .gitlab-ci.yml                                | 12 +--
 .../{biohpc_local.config => biohpc.config}    | 26 ------
 workflow/conf/biohpc_cluster.config           | 88 -------------------
 workflow/conf/cluster.config                  | 31 +++++++
 workflow/conf/local.config                    | 25 ++++++
 workflow/nextflow.config                      | 11 ++-
 6 files changed, 69 insertions(+), 124 deletions(-)
 rename workflow/conf/{biohpc_local.config => biohpc.config} (71%)
 mode change 100755 => 100644
 delete mode 100644 workflow/conf/biohpc_cluster.config
 create mode 100644 workflow/conf/cluster.config
 create mode 100755 workflow/conf/local.config

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b33b296..c0a034f 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -40,7 +40,7 @@ simple_1:
       - develop
       - master
   script:
-  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
   - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
@@ -65,7 +65,7 @@ simple_2:
       - master
       - tags
   script:
-  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
   - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
@@ -89,7 +89,7 @@ detailed_1:
     refs:
       - tags
   script:
-  - nextflow -q run workflow/main.nf -profile biohpc,_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0'
+  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0'
   - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
@@ -114,7 +114,7 @@ detailed_2:
     refs:
       - tags
   script:
-  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
   - pytest -m count302
   artifacts:
     name: "$CI_JOB_NAME"
@@ -138,7 +138,7 @@ detailed_3:
     refs:
       - tags
   script:
-  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
+  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
   - pytest -m count301
   artifacts:
     name: "$CI_JOB_NAME"
@@ -162,7 +162,7 @@ detailed_4:
     refs:
       - tags
   script:
-  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
   - pytest -m count211
   artifacts:
     name: "$CI_JOB_NAME"
diff --git a/workflow/conf/biohpc_local.config b/workflow/conf/biohpc.config
old mode 100755
new mode 100644
similarity index 71%
rename from workflow/conf/biohpc_local.config
rename to workflow/conf/biohpc.config
index 182f03b..7304219
--- a/workflow/conf/biohpc_local.config
+++ b/workflow/conf/biohpc.config
@@ -1,29 +1,3 @@
-process {
-  executor = 'local'
-
-  withLabel: checkDesignFile {
-    module = ['python/3.6.1-2-anaconda']
-  }
-  withLabel: count211 {
-    module = ['cellranger/2.1.1']
-  }
-  withLabel: count301 {
-    module = ['cellranger/3.0.1']
-  }
-  withLabel: count302 {
-    module = ['cellranger/3.0.2']
-  }
-  withLabel: count310 {
-    module = ['cellranger/3.1.0']
-  }
-  withLabel: versions {
-    module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
-  }
-  withLabel: multiqc {
-    module = ['multiqc/1.7']
-  }
-}
-
 params {
   // Reference file paths on BioHPC
   genomes {
diff --git a/workflow/conf/biohpc_cluster.config b/workflow/conf/biohpc_cluster.config
deleted file mode 100644
index d6c7087..0000000
--- a/workflow/conf/biohpc_cluster.config
+++ /dev/null
@@ -1,88 +0,0 @@
-process {
-  executor = 'slurm'
-  queue = '32GB'
-  clusterOptions = '--hold'
-
-  withLabel: checkDesignFile {
-    module = ['python/3.6.1-2-anaconda']
-    queue = '32GB'
-  }
-  withLabel: count211 {
-    module = ['cellranger/2.1.1']
-    queue = '128GB,256GB,256GBv1,384GB'
-  }
-  withLabel: count301 {
-    module = ['cellranger/3.0.1']
-    queue = '128GB,256GB,256GBv1,384GB'
-  }
-  withLabel: count302 {
-    module = ['cellranger/3.0.2']
-    queue = '128GB,256GB,256GBv1,384GB'
-  }
-  withLabel: count310 {
-    module = ['cellranger/3.1.0']
-    queue = '128GB,256GB,256GBv1,384GB'
-  }
-  withLabel: versions {
-    module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
-    queue = '32GB'
-  }
-  withLabel: multiqc {
-    module = ['multiqc/1.7']
-    queue = '32GB'
-  }
-}
-
-params {
-  // Reference file paths on BioHPC
-  genomes {
-    'GRCh38-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'GRCh38-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'mm10-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'mm10-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'GRCh38_and_mm10-3.1.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19_and_mm10-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19_and_mm10-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'ercc92-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-  }
-  // Chemistry mapping parameter
-  chemistry {
-    'auto' {
-      param = 'auto'
-    }
-    '3GEXv1' {
-      param = 'SC3Pv1'
-    }
-   '3GEXv2' {
-      param = 'SC3Pv2'
-    }
-   '3GEXv3' {
-      param = 'SC3Pv3'
-    }
-   '5GEX' {
-      param = 'fiveprime'
-    }
-  }
-}
diff --git a/workflow/conf/cluster.config b/workflow/conf/cluster.config
new file mode 100644
index 0000000..2526210
--- /dev/null
+++ b/workflow/conf/cluster.config
@@ -0,0 +1,31 @@
+process {
+  executor = 'slurm'
+  queue = '32GB'
+  clusterOptions = '--hold'
+
+  withLabel: checkDesignFile {
+    module = ['python/3.6.1-2-anaconda']
+  }
+  withLabel: count211 {
+    module = ['cellranger/2.1.1']
+    queue = '128GB,256GB,256GBv1,384GB'
+  }
+  withLabel: count301 {
+    module = ['cellranger/3.0.1']
+    queue = '128GB,256GB,256GBv1,384GB'
+  }
+  withLabel: count302 {
+    module = ['cellranger/3.0.2']
+    queue = '128GB,256GB,256GBv1,384GB'
+  }
+  withLabel: count310 {
+    module = ['cellranger/3.1.0']
+    queue = '128GB,256GB,256GBv1,384GB'
+  }
+  withLabel: versions {
+    module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
+  }
+  withLabel: multiqc {
+    module = ['multiqc/1.7']
+  }
+}
diff --git a/workflow/conf/local.config b/workflow/conf/local.config
new file mode 100755
index 0000000..556476f
--- /dev/null
+++ b/workflow/conf/local.config
@@ -0,0 +1,25 @@
+process {
+  executor = 'local'
+
+  withLabel: checkDesignFile {
+    module = ['python/3.6.1-2-anaconda']
+  }
+  withLabel: count211 {
+    module = ['cellranger/2.1.1']
+  }
+  withLabel: count301 {
+    module = ['cellranger/3.0.1']
+  }
+  withLabel: count302 {
+    module = ['cellranger/3.0.2']
+  }
+  withLabel: count310 {
+    module = ['cellranger/3.1.0']
+  }
+  withLabel: versions {
+    module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
+  }
+  withLabel: multiqc {
+    module = ['multiqc/1.7']
+  }
+}
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 527b3ca..1cfa59d 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -1,9 +1,12 @@
 profiles {
-  biohpc_local {
-    includeConfig 'conf/biohpc_local.config'
+  biohpc {
+    includeConfig 'conf/biohpc.config'
   }
-  biohpc_cluster {
-    includeConfig 'conf/biohpc_cluster.config'
+  local {
+    includeConfig 'conf/local.config'
+  }
+  cluster {
+    includeConfig 'conf/cluster.config'
   }
   aws {
     includeConfig 'conf/aws.config'
-- 
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