[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -4,7 +4,8 @@ exclude: |
   (?x)(
       ^assets/|
       ^docs/.*.html|
-      ^_extensions/
+      ^_extensions/|
+      ^.*\.bed
    )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -32,7 +33,7 @@ repos:
       - id: black
   # R formatting
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9026
+    rev: v0.4.3.9028
     hooks:
       - id: style-files
   # general linting

docs/pipeline-details/output.md

@@ -119,7 +119,7 @@ VCF/
 .   .
 .   .
 │   └── raw_variants.chrN.vcf.gz[.tbi]
-├── indel.filterd.vcf.gz[.tbi]
+├── indel.filtered.vcf.gz[.tbi]
 ├── {sample1}-normal.germline.vcf.gz[.tbi]
 ├── {sample1}-tumor.germline.vcf.gz[.tbi]
 .

docs/usage/cache.md

@@ -6,7 +6,7 @@ The `xavier` executable is composed of several inter-related sub commands. Pleas
 
 This part of the documentation describes options and concepts for <code>xavier <b>cache</b></code> sub command in more detail. With minimal configuration, the **`cache`** sub command enables you to cache remote resources for the xavier pipeline. Caching remote resources allows the pipeline to run in an offline mode. The cache sub command can also be used to pull our pre-built reference bundles onto a new cluster or target system.
 
-The cache sub command creates local cache on the filesysytem for resources hosted on DockerHub or AWS S3. These resources are normally pulled onto the filesystem when the pipeline runs; however, due to network issues or DockerHub pull rate limits, it may make sense to pull the resources once so a shared cache can be created and re-used. It is worth noting that a singularity cache cannot normally be shared across users. Singularity strictly enforces that its cache is owned by the user. To get around this issue, the cache subcommand can be used to create local SIFs on the filesystem from images on DockerHub.
+The cache sub command creates local cache on the filesysytem for resources hosted on DockerHub or AWS S3. These resources are normally pulled onto the filesystem when the pipeline runs; however, due to network issues or DockerHub pull rate limits, it may make sense to pull the resources once so a shared cache can be created and reused. It is worth noting that a singularity cache cannot normally be shared across users. Singularity strictly enforces that its cache is owned by the user. To get around this issue, the cache subcommand can be used to create local SIFs on the filesystem from images on DockerHub.
 
 ## 2. Synopsis
 

docs/usage/gui.md

@@ -120,7 +120,7 @@ XAVIER pipeline can be run in two different modes:\
 
 #### 3.3a Tumor-normal pair analysis
 
-In case of tumor-normal pairs, a tab-delimited text file is neeed that contains the list of normal and tumor samples. For example,
+In case of tumor-normal pairs, a tab-delimited text file is needed that contains the list of normal and tumor samples. For example,
 
 ```bash
 Normal  Tumor

docs/usage/run.md

@@ -279,7 +279,7 @@ xavier run --input tests/data/*.R?.fastq.gz \
 
 The example dataset in `tests/data` in this repository is a very small
 subsampled dataset, and some steps of the pipeline fail due to the small size
-(CNV callling, somalier, etc).
+(CNV calling, somalier, etc).
 We have a larger subsample (25% of a full human dataset) available on Biowulf if
 you would like to test the full functionality of the pipeline:
 `/data/CCBR_Pipeliner/testdata/XAVIER/human_subset/*.R?.fastq.gz`

resources/cacher

@@ -11,7 +11,7 @@ how subsequent resources are pulled onto the cluster's filesystem. cacher utiliz
 to avoid pull into resources on a compute node but support for additional job schedulers
 (i.e. PBS, SGE, LSF, Tibanna) may be added in the near future.
   The main entry point of the pipeline 'xavier' calls this job submission wrapper script.
-As so, this script can be used to manually by-pass 'xavier' for a previously failed cache.
+As so, this script can be used to manually bypass 'xavier' for a previously failed cache.
   Please Note: it is highly recommended to use 'xavier'; it is the main entry point
 and preferred entry point of the XAVIER pipeline. If you are experience error, it
 maybe due to improperly mounting singularity bind paths which 'xavier' will internally
@@ -155,7 +155,7 @@ function _pull(){
 
   # Goto Pipeline Output directory
   # Create a local singularity cache in output directory
-  # cache can be re-used instead of re-pulling from DockerHub every time
+  # cache can be reused instead of re-pulling from DockerHub every time
   cd "$2" && export SINGULARITY_CACHEDIR="${3}"
 
   # unsetting XDG_RUNTIME_DIR to avoid some unsighly but harmless warnings

resources/runner

@@ -19,7 +19,7 @@ submitted to the cluster via the job scheduler, SLURM. Support for
 additional job schedulers (i.e. PBS, SGE, LSF, Tibanna) may be added
 in the future.
   The main entry point of the pipeline 'xavier' calls this job
-submission wrapper script. As so, this script can be used to by-pass
+submission wrapper script. As so, this script can be used to bypass
 'xavier' for a previously failed run; meaning, it can be used to
 re-run the pipeline to pick back off where the last failure occurred
 or re-start the pipeline.
@@ -52,7 +52,7 @@ Required Arguments:
                                  and aggregates bind paths to mount to the
                                  container's filesystem.
                                  If you are manually running this script
-                                 or by-passing xavier, you will need
+                                 or bypassing xavier, you will need
                                  to provide the bind paths of the rawdata
                                  directory(s) along with the pipeline's
                                  output directory and any directories for
@@ -182,7 +182,7 @@ function submit(){
 
   # Goto Pipeline Output directory
   # Create a local singularity cache in output directory
-  # cache can be re-used instead of re-pulling from DockerHub every time
+  # cache can be reused instead of re-pulling from DockerHub every time
   cd "$3" && export SINGULARITY_CACHEDIR="${5}"
 
   # unsetting XDG_RUNTIME_DIR to avoid some unsighly but harmless warnings
@@ -273,7 +273,7 @@ EOF
         ;;
     esac
 
-  # Return exit-code of pipeline sumbission
+  # Return exit-code of pipeline submission
   echo "$job_id"
 }
 

src/xavier/__main__.py

@@ -501,7 +501,7 @@ def parsed_arguments():
         default:  '/lscratch/$SLURM_JOBID/'",
     )
 
-    # Number of threads for the xavier pipeline's main proceess
+    # Number of threads for the xavier pipeline's main process
     subparser_run.add_argument(
         "--threads",
         type=int,

src/xavier/shells.py

@@ -43,7 +43,7 @@ def bash(
         Shell command to run
     @param interpreter <str>:
         Interpreter for command to run [default: bash]
-    @pararm strict <bool>:
+    @param strict <bool>:
         Prefixes any command with 'set -euo pipefail' to ensure process fail with
         the expected exit-code
     @params kwargs <check_call()>:

workflow/rules/germline.smk

@@ -162,7 +162,7 @@ rule Gatk_Variantfilter:
     input:
         vcf = os.path.join(output_germline_base,"VCF","raw_variants.vcf.gz"),
     output:
-       indelvcf = os.path.join(output_germline_base,"VCF","indel.filterd.vcf.gz"),
+       indelvcf = os.path.join(output_germline_base,"VCF","indel.filtered.vcf.gz"),
        snpvcf = os.path.join(output_germline_base,"VCF","snp.filtered.vcf.gz"),
        vcf = os.path.join(output_germline_base,"VCF","snp_indel.filtered.vcf.gz")
 

workflow/rules/qc.smk

@@ -407,7 +407,7 @@ if config['project']['annotation'] in ['hg38', 'hg38_noalt']:
         @Input:
             Mapped and pre-processed BAM file
         @Output:
-            Exracted sites in (binary) somalier format
+            Extracted sites in (binary) somalier format
         """
         input:
             bam = os.path.join(output_bamdir,"final_bams","{samples}.bam"),
@@ -435,7 +435,7 @@ if config['project']['annotation'] in ['hg38', 'hg38_noalt']:
         compare across all samples. This step also runs the ancestry estimation
         function in Somalier.
         @Input:
-            Exracted sites in (binary) somalier format for ALL samples in the cohort
+            Extracted sites in (binary) somalier format for ALL samples in the cohort
         @Output:
             Separate tab-separated value (TSV) files with relatedness and ancestry outputs
         """
@@ -537,7 +537,7 @@ if config['project']['annotation']=='mm10':
         @Input:
             Mapped and pre-processed BAM file
         @Output:
-            Exracted sites in (binary) somalier format
+            Extracted sites in (binary) somalier format
         """
         input:
             bam = os.path.join(output_bamdir,"final_bams","{samples}.bam"),
@@ -565,7 +565,7 @@ if config['project']['annotation']=='mm10':
         compare across all samples. This step also runs the ancestry estimation
         function in Somalier.
         @Input:
-            Exracted sites in (binary) somalier format for ALL samples in the cohort
+            Extracted sites in (binary) somalier format for ALL samples in the cohort
         @Output:
             Separate tab-separated value (TSV) files with relatedness and ancestry outputs
         """

workflow/scripts/RScripts/combineAllSampleCompareResults.R

@@ -9,15 +9,14 @@ user.input.3 <- args[2]
 somaliaDistance <- read.table(user.input.1, sep = "\t", header = F)
 # somaliaDistance<-read.table("~/relatedness.pairs.tsv",sep = "\t",header = F)
 predictedPairs <- list()
-for (sample in sort(unique(c(somaliaDistance$V1, somaliaDistance$V2))))
-{
-  samplePairs <- somaliaDistance %>% dplyr::filter(V1 %in% sample | V2 %in% sample)
+for (sample in sort(unique(c(somaliaDistance$V1, somaliaDistance$V2)))) {
+  samplePairs <- somaliaDistance %>%
+    dplyr::filter(V1 %in% sample | V2 %in% sample)
   maxRelatedess <- which(samplePairs$V3 == max(samplePairs$V3, na.rm = T))
   maxHomCon <- which(samplePairs$V6 == max(samplePairs$V6, na.rm = T))
   m <- intersect(maxRelatedess, maxHomCon)
   if (length(m) > 0) {
-    for (i in m)
-    {
+    for (i in m) {
       if (sample == unlist(samplePairs[i, ]$V2)) {
         t <- unlist(samplePairs[i, c(2, 1, 3, 6)])
         names(t) <- NULL
@@ -27,10 +26,12 @@ for (sample in sort(unique(c(somaliaDistance$V1, somaliaDistance$V2))))
       }
     }
   } else {
-    print(paste0("No consensous between the Relatedness and Homology for sample:", sample))
+    print(paste0(
+      "No consensous between the Relatedness and Homology for sample:",
+      sample
+    ))
     maxVal <- c(maxRelatedess, maxHomCon)
-    for (i in maxVal)
-    {
+    for (i in maxVal) {
       if (sample == unlist(samplePairs[i, ]$V2)) {
         t <- unlist(samplePairs[i, c(2, 1, 3, 6)])
         names(t) <- NULL
@@ -42,7 +43,12 @@ for (sample in sort(unique(c(somaliaDistance$V1, somaliaDistance$V2))))
   }
 }
 finalPredPairs <- data.frame(do.call("rbind", predictedPairs))
-colnames(finalPredPairs) <- c("Sample1", "Sample2", "Som:relatedness", "Som:hom_concordance")
+colnames(finalPredPairs) <- c(
+  "Sample1",
+  "Sample2",
+  "Som:relatedness", # codespell:ignore-line
+  "Som:hom_concordance" # codespell:ignore-line
+) # codespell:ignore-line
 
 # VerifyBAMID
 # verifyBAMID<-read.table(user.input.2,sep = "\t",header = T)
@@ -72,4 +78,10 @@ colnames(finalPredPairs) <- c("Sample1", "Sample2", "Som:relatedness", "Som:hom_
 ## Combine the output from both the tools
 # mergedDF<-merge(x=finalPredPairs,y=finalpredictedPairsVerifyBAMID,by = "Sample1",all = TRUE)
 # write.table(mergedDF[,c(1:4,6)],file = user.input.3,sep = "\t",quote = FALSE,row.names = FALSE)
-write.table(finalPredPairs, file = user.input.3, sep = "\t", quote = FALSE, row.names = FALSE)
+write.table(
+  finalPredPairs,
+  file = user.input.3,
+  sep = "\t",
+  quote = FALSE,
+  row.names = FALSE
+)