small fixes to configs

RaqManzano · Mar 19, 2024 · f22561b · f22561b
1 parent 8b919b3
commit f22561b
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Showing 4 changed files with 997 additions and 982 deletions.
diff --git a/assets/samplesheet2.csv b/assets/samplesheet2.csv
@@ -1,4 +1,4 @@
-patient,status,sample,lane,fastq_1,fastq_2,bam,bai,cram,crai,table,vcf
-P01,0,SAMPLE_NORMAL,L01,/path/to/fastq/files/AEG588A1_S1_L001_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L001_R2_001.fastq.gz,,,,,,,
-P01,1,SAMPLE_TUMOR,L01,/path/to/fastq/files/AEG588A4_S1_L001_R1_001.fastq.gz,/path/to/fastq/files/AEG588A4_S1_L001_R2_001.fastq.gz,,,,,,,
-P01,2,SAMPLE_RNA,L01,/path/to/fastq/files/AEG588A6_S1_L001_R1_001.fastq.gz,/path/to/fastq/files/AEG588A6_S1_L001_R2_001.fastq.gz,,,,,,,
+patient,status,sample,lane,fastq_1,fastq_2
+P01,0,SAMPLE_NORMAL,L01,/path/to/fastq/files/AEG588A1_S1_L001_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L001_R2_001.fastq.gz
+P01,1,SAMPLE_TUMOR,L01,/path/to/fastq/files/AEG588A4_S1_L001_R1_001.fastq.gz,/path/to/fastq/files/AEG588A4_S1_L001_R2_001.fastq.gz
+P01,2,SAMPLE_RNA,L01,/path/to/fastq/files/AEG588A6_S1_L001_R1_001.fastq.gz,/path/to/fastq/files/AEG588A6_S1_L001_R2_001.fastq.gz
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -19,7 +19,9 @@ params {
     max_time   = '8.h'
 
     // Input data
-    input = "${projectDir}/tests/csv/3.0/fastq_triplet.csv"
+    input  = "${projectDir}/tests/csv/3.0/fastq_triplet.csv"
+    outdir = 'rnadnavar_test_full'
+
     // Small reference genome
     wes               = true
     genome            = 'GRCh38'

diff --git a/nextflow.config b/nextflow.config
@@ -24,13 +24,19 @@ params {
     save_reference                  = false
     build_only_index                = false // Only build the reference indexes
     download_cache                  = false // Do not download annotation cache
+    fasta_fai                       = null
+    dict                            = null
+
 
 
     // Sequence read information
     read_length                     = 76 // Required for STAR to build index and align reads TODO: automate
     wes                             = false       // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers
 
     // Alignment
+    bwa                             = null
+    bwamem2                         = null
+    star_index                      = null
     aligner                         = 'bwa-mem'    // Only STAR is currently supported.
     star_twopass                    = true
     star_ignore_sjdbgtf             = false     // Ignore GTF file while creating index or alignment by STAR
@@ -48,6 +54,7 @@ params {
     save_mapped                     = false      // Mapped BAMs not saved
     hisat2_index                    = null
     dragmap                         = null
+    gff                             = null
 
 
     // Modify fastqs (trim/split) with FASTP
@@ -61,12 +68,18 @@ params {
     save_trimmed        = false
     save_split_fastqs   = false
 
+    exon_bed            = null
+
     // Variant calling
     no_intervals                    = false
     intervals                       = null
     nucleotides_per_second          = 200000 // Default interval size
     germline_resource               = null
     germline_resource_tbi           = null
+    dbsnp                           = null
+    dbsnp_tbi                       = null
+    known_indels                    = null
+    known_indels_tbi                = null
     known_snps                      = null
     known_snps_tbi                  = null
     pon                             = null
@@ -85,8 +98,8 @@ params {
     ignore_soft_clipped_bases       = true
 
     // Variant annotation
-    tools                           = null  // No default Variant_Calling or Annotation tools
-    genesplicer                     = null // genesplicer disabled within VEP
+    tools                     = null  // No default Variant_Calling or Annotation tools
+    genesplicer               = null // genesplicer disabled within VEP
     dbnsfp                    = null // No dbnsfp processed file
     dbnsfp_consequence        = null // No default consequence for dbnsfp plugin
     dbnsfp_fields             = "rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF" // Default fields for dbnsfp plugin
@@ -95,14 +108,17 @@ params {
     spliceai_indel_tbi        = null // No spliceai_indel file index
     spliceai_snv              = null // No spliceai_snv file
     spliceai_snv_tbi          = null // No spliceai_snv file index
-    vep_custom_args= "--no_progress --offline --shift_hgvs 1 --check_existing --tsl --domains --total_length --allele_number --no_escape --xref_refseq --failed 1 --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --format vcf --biotype --force_overwrite --sift p --polyphen p --variant_class --regulatory --allele_number --af_gnomad --af_gnomadg --gene_phenotype --hgvs --hgvsg --max_af"
+    vep_custom_args           = "--no_progress --offline --shift_hgvs 1 --check_existing --tsl --domains --total_length --allele_number --no_escape --xref_refseq --failed 1 --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --format vcf --biotype --force_overwrite --sift p --polyphen p --variant_class --regulatory --allele_number --af_gnomad --af_gnomadg --gene_phenotype --hgvs --hgvsg --max_af"
     vep_cache                 = null // No directory for VEP cache
     vep_include_fasta         = false // Don't use fasta file for annotation with VEP
-    vep_dbnsfp                      = null
-    vep_loftee                      = null
-    vep_spliceai                    = null
-    vep_spliceregion                = null
-    vep_out_format                  = 'vcf'
+    vep_dbnsfp                = null
+    vep_loftee                = null
+    vep_spliceai              = null
+    vep_spliceregion          = null
+    vep_out_format            = 'vcf'
+    vep_cache_version         = '110'
+    vep_species               = 'homo_sapiens'
+    vep_genome                = null
     outdir_cache              = null // No default outdir cache
 
     //filtering