chore: Merge branch 'main' of https://github.com/CCBR/CHAMPAGNE

CCBR · Jan 26, 2024 · 005f637 · 005f637
2 parents 0db5ea2 + 442fbae
commit 005f637
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Showing 9 changed files with 35 additions and 16 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,12 @@
 ## CHAMPAGNE development version
 
+- Fix configuration files for compatibility with using the GitHub repo as the source. (#173, @kelly-sovacool)
+  - These equivalent commands now work:
+    ```sh
+    nextflow run CCBR/CHAMPAGNE
+    champagne run --main CCBR/CHAMPAGNE
+    ```
+
 ## CHAMPAGNE 0.3.0
 
 ### New features

diff --git a/conf/biowulf.config b/conf/biowulf.config
@@ -12,7 +12,7 @@ params {
     // CCBR shared resource paths
     index_dir = '/data/CCBR_Pipeliner/db/PipeDB/Indices'
     fastq_screen {
-        conf = "assets/fastq_screen_biowulf.conf"
+        conf = "${projectDir}/assets/fastq_screen_biowulf.conf"
         db_dir = '/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen_db/'
     }
 }

diff --git a/conf/frce.config b/conf/frce.config
@@ -7,7 +7,7 @@ params {
     // CCBR shared resource paths
     index_dir = null // TODO
     fastq_screen {
-        conf = "assets/fastq_screen_frce.conf" // TODO
+        conf = "${projectDir}/assets/fastq_screen_frce.conf" // TODO
         db_dir = null // TODO
     }
 }

diff --git a/conf/full_mm10.config b/conf/full_mm10.config
@@ -4,8 +4,8 @@ params {
 
     genome = 'mm10'
     outdir = "results/full_mm10"
-    input = "assets/samplesheet_full_mm10.csv"
-    contrasts = 'assets/contrasts_full_mm10.yml'
+    input = "${projectDir}/assets/samplesheet_full_mm10.csv"
+    contrasts = "${projectDir}/assets/contrasts_full_mm10.yml"
     sicer {
         species = "mm10" // supported species https://github.com/zanglab/SICER2/blob/master/sicer/lib/GenomeData.py
     }

diff --git a/conf/genomes.config b/conf/genomes.config
@@ -9,7 +9,7 @@ params {
             chrom_sizes = "${params.index_dir}/hg38_basic/indexes/hg38.fa.sizes"
             gene_info = "${params.index_dir}/hg38_basic/geneinfo.bed"
             effective_genome_size = 2700000000
-            meme_motifs = 'assets/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz' // source https://github.com/CCBR/ASPEN/raw/55f909d76500c3502c1c397ef3000908649b0284/resources/motif/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz
+            meme_motifs = "${projectDir}/assets/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz" // source https://github.com/CCBR/ASPEN/raw/55f909d76500c3502c1c397ef3000908649b0284/resources/motif/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz
             bioc_txdb = 'TxDb.Hsapiens.UCSC.hg38.knownGene'
             bioc_annot = 'org.Hs.eg.db'
         }
@@ -22,7 +22,7 @@ params {
             chrom_sizes = "${params.index_dir}/mm10_basic/indexes/mm10.fa.sizes"
             gene_info = "${params.index_dir}/mm10_basic/geneinfo.bed"
             effective_genome_size = 2400000000
-            meme_motifs = 'assets/HOCOMOCOv11_core_MOUSE_mono_meme_format.tar.gz' // source https://github.com/CCBR/ASPEN/raw/55f909d76500c3502c1c397ef3000908649b0284/resources/motif/HOCOMOCOv11_core_MOUSE_mono_meme_format.tar.gz
+            meme_motifs = "${projectDir}/assets/HOCOMOCOv11_core_MOUSE_mono_meme_format.tar.gz" // source https://github.com/CCBR/ASPEN/raw/55f909d76500c3502c1c397ef3000908649b0284/resources/motif/HOCOMOCOv11_core_MOUSE_mono_meme_format.tar.gz
             bioc_txdb = 'TxDb.Mmusculus.UCSC.mm10.knownGene'
             bioc_annot = 'org.Mmu.eg.db'
         }

diff --git a/conf/test.config b/conf/test.config
@@ -3,8 +3,8 @@ params {
     config_profile_description = 'Minimal test dataset to check paired & single end handling'
 
     outdir = 'results/test'
-    input = 'assets/samplesheet_test.csv' // adapted from 'https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/samplesheet/v2.0/samplesheet_test.csv'
-    //contrasts = 'assets/contrasts_test.yml' // diffbind DESeq2 fails on this test data
+    input = "${projectDir}/assets/samplesheet_test.csv" // adapted from 'https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/samplesheet/v2.0/samplesheet_test.csv'
+    //contrasts = "${projectDir}/assets/contrasts_test.yml" // diffbind DESeq2 fails on this test data
 
     genome = 'sacCer3'
     read_length = 50
@@ -13,7 +13,7 @@ params {
     genome_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa'
     genes_gtf   = 'https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf'
     blacklist = '/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/indexes/hg38.blacklist_v3.chrM.chr_rDNA.fa'
-    rename_contigs = 'assets/R64-1-1_ensembl2UCSC.txt'
+    rename_contigs = "${projectDir}/assets/R64-1-1_ensembl2UCSC.txt"
     meme_motifs = null
     bioc_txdb = 'TxDb.Scerevisiae.UCSC.sacCer3.sgdGene'
     bioc_annot = 'org.Sc.sgd.db'

diff --git a/conf/test_mm10.config b/conf/test_mm10.config
@@ -4,8 +4,8 @@ params {
 
     genome = 'mm10'
     outdir = "results/test_mm10"
-    input = "assets/samplesheet_test_mm10.csv"
-    contrasts = 'assets/contrasts_test_mm10.yml'
+    input = "${projectDir}/assets/samplesheet_test_mm10.csv"
+    contrasts = "${projectDir}/assets/contrasts_test_mm10.yml"
     read_length = 50
     sicer.species = "mm10" // supported species https://github.com/zanglab/SICER2/blob/master/sicer/lib/GenomeData.py
 

diff --git a/docs/nextflow.md b/docs/nextflow.md
@@ -9,7 +9,7 @@ as the config files will be accessed directly from the GitHub repo.
 nextflow run CCBR/CHAMPAGNE -profile test,singularity
 ```
 
-You can specify a specific version, tag, or branch with `-r`:
+You can specify a specific version, tag, or branch on [GitHub](https://github.com/CCBR/CHAMPAGNE) with `-r`:
 
 ```sh
 nextflow run CCBR/CHAMPAGNE -r v0.3.0 -profile test,singularity
@@ -21,3 +21,15 @@ Create and use a custom reference genome:
 nextflow run CCBR/CHAMPAGNE -profile test -entry MAKE_REFERENCE
 nextflow run CCBR/CHAMPAGNE -profile test -c results/test/genome/custom_genome.config
 ```
+
+## biowulf
+
+If you're running it on biowulf without the `champagne` CLI,
+first load the ccbrpipeliner and nextflow modules,
+and be sure to specify the `biowulf` and `slurm` profiles:
+
+```sh
+module load ccbrpipeliner
+module load nextflow
+nextflow run CCBR/CHAMPAGNE -profile test,biowulf,slurm
+```
diff --git a/nextflow.config b/nextflow.config
@@ -40,14 +40,14 @@ params {
     }
 
     multiqc {
-        config = "assets/multiqc_config.yaml"
-        logo = "assets/ccbr_logo.png"
+        config = "${projectDir}/assets/multiqc_config.yaml"
+        logo = "${projectDir}/assets/ccbr_logo.png"
     }
 
     min_fragment_length = 200 // https://github.com/CCBR/Pipeliner/blob/86c6ccaa3d58381a0ffd696bbf9c047e4f991f9e/Rules/InitialChIPseqQC.snakefile#L539
 
     gem {
-        read_dists = 'assets/gem/Read_Distribution_default.txt' // source https://groups.csail.mit.edu/cgs/gem/download/Read_Distribution_default.txt
+        read_dists = "${projectDir}/assets/gem/Read_Distribution_default.txt" // source https://groups.csail.mit.edu/cgs/gem/download/Read_Distribution_default.txt
         fold = 3
         k_min = 6
         k_max = 13
@@ -67,7 +67,7 @@ params {
     }
     homer {
         de_novo = true
-        jaspar_db = 'assets/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt' // source https://jaspar.genereg.net/download/data/2022/CORE/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt
+        jaspar_db = "${projectDir}/assets/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt" // source https://jaspar.genereg.net/download/data/2022/CORE/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt
     }
 
     diffbind {