Rlib and config updates

conf/quest.config

@@ -2,11 +2,11 @@
 // Configuration for Quest (slurm)
 
 
-process {
+// process {
 
-    conda = "/projects/b1059/software/conda_envs/concordance-nf_env"
-    module = 'R/3.6.0'
-}
+//     conda = "/projects/b1059/software/conda_envs/concordance-nf_env"
+//     module = 'R/3.6.0'
+// }
 
 params {
 

conf/quest_debug.config

@@ -1,7 +1,7 @@
 
 // For quest debug
 
-singularity { singularity.enabled = true }
+// singularity { singularity.enabled = true }
 
 process {
 
@@ -14,18 +14,18 @@ process {
 // }
 
 //     container  = 'docker://faithman/concordance:latest'
-    module = "R/3.6.0"
+    // module = "R/3.6.0"
 
 }
 
 params {
     debug = true
     date = new Date().format( 'yyyyMMdd' )
-    genome = "WS245"
+    genome = "WS283"
     fq_file_prefix = "test_data"
     params.out = "DEBUG_concordance-${date}"
     //reference = "WS245/WS245.fa.gz"
-    reference = "/projects/b1059/data/genomes/c_elegans/${genome}"
+    // reference = "/projects/b1059/data/genomes/c_elegans/${genome}"
     fq_file = 'test_data/sample_sheet.tsv'
 
     min_depth = 0

main.nf

@@ -19,9 +19,7 @@ date = new Date().format( 'yyyyMMdd' )
 params.out = "concordance-${date}"
 params.debug = false
 params.help = false
-//params.info_sheet = "(required)"
 params.species == "c_elegans"
-params.R_libpath = "/projects/b1059/software/R_lib_3.6.0"
 
 
 // Debug
@@ -95,16 +93,18 @@ workflow {
     vcf_index = Channel.fromPath("${params.vcf}.tbi") // make sure the index format is consistent in process inputs
     bam_coverage = Channel.fromPath("${params.bam_coverage}")
 
+    hard_filtered_vcf.combine(vcf_index) | (calculate_gtcheck)
 
-if (params.species == "c_elegans") {
+// moved npr1 allele check to alignment
+// if (params.species == "c_elegans") {
 
-    hard_filtered_vcf.combine(vcf_index) | (calculate_gtcheck & npr1_allele_check)
+//     hard_filtered_vcf.combine(vcf_index) | (calculate_gtcheck & npr1_allele_check)
 
-} else {
+// } else {
 
-    hard_filtered_vcf.combine(vcf_index) | (calculate_gtcheck)
+//     hard_filtered_vcf.combine(vcf_index) | (calculate_gtcheck)
 
-}
+// }
 
 
     calculate_gtcheck.out.combine(bam_coverage)
@@ -137,10 +137,7 @@ process get_species_sheet {
         file("*.tsv")
 
     """
-    # add R_libpath to .libPaths() into the R script, create a copy into the NF working directory 
-    echo ".libPaths(c(\\"${params.R_libpath}\\", .libPaths() ))" | cat - ${workflow.projectDir}/bin/download_google_sheet.R > download_google_sheet.R 
-
-    Rscript --vanilla download_google_sheet.R ${params.species}
+    Rscript --vanilla ${workflow.projectDir}/bin/download_google_sheet.R ${params.species}
         
     """
 
@@ -184,11 +181,8 @@ process process_concordance_results {
         file("problem_strains.tsv")
 
     """
-    # add R_libpath to .libPaths() into the R script, create a copy into the NF working directory 
-    echo ".libPaths(c(\\"${params.R_libpath}\\", .libPaths() ))" | cat - ${workflow.projectDir}/bin/process_concordance.R > process_concordance.R 
-
     # Run concordance analysis
-    Rscript --vanilla process_concordance.R SM_coverage.tsv WI_info_sheet.tsv ${params.concordance_cutoff}
+    Rscript --vanilla ${workflow.projectDir}/bin/process_concordance.R SM_coverage.tsv WI_info_sheet.tsv ${params.concordance_cutoff}
     """
 }
 
@@ -228,10 +222,8 @@ process within_group_pairwise {
         isotype = pair_group[2]
 
     """
-        echo ".libPaths(c(\\"${params.R_libpath}\\", .libPaths() ))" | cat - ${workflow.projectDir}/bin/plot_pairwise.R > plot_pairwise.R 
-
         bcftools query -f '%CHROM\t%POS[\t%GT]\n' -s ${pair} concordance.vcf.gz > out.tsv
-        Rscript --vanilla plot_pairwise.R ${pair} ${group} ${isotype}
+        Rscript --vanilla ${workflow.projectDir}/bin/plot_pairwise.R ${pair} ${group} ${isotype}
 
     """
 }
@@ -327,32 +319,32 @@ process between_group_pairwise {
         sp2 = pair_group[1]
 
     """  
-        echo ".libPaths(c(\\"${params.R_libpath}\\", .libPaths() ))" | cat - ${workflow.projectDir}/bin/process_strain_pairwise.R > process_strain_pairwise.R           
         csvtk cut -t -f CHROM,POS,${sp1},${sp2} out_gt.tsv > ${sp1}-${sp2}.queried.tsv
-        Rscript --vanilla process_strain_pairwise.R ${sp1} ${sp2} ${sp1}-${sp2}.queried.tsv
+        Rscript --vanilla ${workflow.projectDir}/bin/process_strain_pairwise.R ${sp1} ${sp2} ${sp1}-${sp2}.queried.tsv
         mv condition_results.tsv ${sp1}-${sp2}.tsv
         mv for_distribution.tsv ${sp1}-${sp2}-distribution.tsv
         rm ${sp1}-${sp2}.queried.tsv
     """
 }
 
-process npr1_allele_check {
+// Moved this process to alignment now
+// process npr1_allele_check {
 
-    cpus params.cores
+//     cpus params.cores
 
-    publishDir "${params.out}/concordance", mode: 'copy', overwrite: true
+//     publishDir "${params.out}/concordance", mode: 'copy', overwrite: true
 
-    input:
-        tuple file("concordance.vcf.gz"), file("concordance.vcf.gz.tbi") //from npr1_allele
+//     input:
+//         tuple file("concordance.vcf.gz"), file("concordance.vcf.gz.tbi") //from npr1_allele
 
-    output:
-        file("npr1_allele_strain.tsv") //into npr1_out
+//     output:
+//         file("npr1_allele_strain.tsv") //into npr1_out
 
-    """
-        echo -e 'problematic_strain\\tgt' > npr1_allele_strain.tsv
-        bcftools view --threads ${params.cores} -t X:4768788 concordance.vcf.gz | bcftools query -f '[%SAMPLE\\t%GT\\n]' | awk '\$2 != "1/1"' >> npr1_allele_strain.tsv
-    """
-}
+//     """
+//         echo -e 'problematic_strain\\tgt' > npr1_allele_strain.tsv
+//         bcftools view --threads ${params.cores} -t X:4768788 concordance.vcf.gz | bcftools query -f '[%SAMPLE\\t%GT\\n]' | awk '\$2 != "1/1"' >> npr1_allele_strain.tsv
+//     """
+// }
 
 process merge_betweengroup_pairwise_output {
 
@@ -402,8 +394,7 @@ process combine_pairwise_results {
         file("new_isotype_groups.tsv")
 
     """
-        echo ".libPaths(c(\\"${params.R_libpath}\\", .libPaths() ))" | cat - ${workflow.projectDir}/bin/merge_groups_info.R > merge_groups_info.R           
-        Rscript --vanilla merge_groups_info.R isotype_groups.tsv merge_betweengroup_pairwise_output.tsv npr1_allele_strain.tsv
+        Rscript --vanilla ${workflow.projectDir}/bin/merge_groups_info.R isotype_groups.tsv merge_betweengroup_pairwise_output.tsv npr1_allele_strain.tsv
     """
 }
 

nextflow.config

@@ -63,3 +63,14 @@ dag {
     file = "${params.tracedir}/${params.timestamp}_dag.svg"
 }
 
+singularity {
+
+    enabled = true
+    autoMounts = true
+
+    cacheDir = "/projects/b1059/singularity"
+    pullTimeout = '20 min'
+}
+
+process.container = 'andersenlab/concordance'
+