Merge pull request #126 from MaxUlysse/FixLink

Fix typos

Author: maxulysse

conf/igenomes.config

@@ -53,14 +53,14 @@ params {
       bwa                      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
       chr_dir                  = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Chromosomes"
       chr_length               = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Length/GRCm38.len"
-      dbsnp                    = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/Annotation/mgp.v5.merged.snps_all.dbSNP142.vcf.gz"
-      dbsnp_index              = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/Annotation/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi"
+      dbsnp                    = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz"
+      dbsnp_index              = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi"
       dict                     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.dict"
       fasta                    = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
       fasta_fai                = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa.fai"
       intervals                = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/intervals/GRCm38_calling_list.bed"
-      known_indels             = "${params.igenomes_base}/Mus_musculus/Annotation/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz"
-      known_indels_index       = "${params.igenomes_base}/Mus_musculus/Annotation/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
+      known_indels             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz"
+      known_indels_index       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
       snpeff_db                = 'GRCm38.86'
       species                  = 'mus_musculus'
       vep_cache_version        = '98'

docs/input.md

@@ -5,15 +5,15 @@
 Input files for Sarek can be specified using a TSV file given to the `--input` command.
 The TSV file is a Tab Separated Value file with columns:
 
-- `subject gender status sample lane fastq1 fastq2` for step `mapping` with paired-end FASTQs
-- `subject gender status sample lane bam` for step `mapping` with unmapped BAMs
-- `subject gender status sample bam bai recaltable` for step `recalibrate` with BAMs
-- `subject gender status sample bam bai` for step `variantcalling` with BAMs
+- `subject sex status sample lane fastq1 fastq2` for step `mapping` with paired-end FASTQs
+- `subject sex status sample lane bam` for step `mapping` with unmapped BAMs
+- `subject sex status sample bam bai recaltable` for step `recalibrate` with BAMs
+- `subject sex status sample bam bai` for step `variantcalling` with BAMs
 
 The content of these columns is quite straight-forward:
 
 - `subject` designate the subject, it should be the ID of the Patient, and it must design only one patient
-- `gender` is the gender of the Patient, (XX or XY)
+- `sex` are the sex chromosomes of the Patient, (XX or XY)
 - `status` is the status of the Patient, (0 for Normal or 1 for Tumor)
 - `sample` designate the Sample, it should be the ID of the sample (it is possible to have more than one tumor sample for each patient, i.e. a tumor and a relapse), it must design only one sample
 - `lane` is used when the sample is multiplexed on several lanes, it must be unique for each lane in the same sample