Merge pull request #373 from genomic-medicine-sweden/fixes

Update schema, output.md, and remove unused parameters

docs/output.md

@@ -76,27 +76,27 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 ##### Picard's MarkDuplicates
 
-[Picard MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates) is used for marking PCR duplicates that can occur during library amplification. This is essential as the presence of such duplicates results in false inflated coverages, which in turn can lead to overly-confident genotyping calls during variant calling. Only reads aligned by Bwa-mem2 are processed by this tool.
+[Picard MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates) is used for marking PCR duplicates that can occur during library amplification. This is essential as the presence of such duplicates results in false inflated coverages, which in turn can lead to overly-confident genotyping calls during variant calling. Only reads aligned by Bwa-mem2 are processed by this tool. By default, alignment files are published in bam format. If you would like to store cram files instead, set `--save_mapped_as_cram` to true.
 
 <details markdown="1">
 <summary>Output files from Alignment</summary>
 
 - `{outputdir}/alignment/`
-  - `*.bam`: Bam file containing report containing quality metrics.
-  - `*.bai`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
+  - `*.bam|*.cram`: Alignment file in bam/cram format.
+  - `*.bai|*.crai`: Index of the corresponding bam/cram file.
   - `*.txt`: Text file containing the dedup metrics.
   </details>
 
 ##### Sentieon Dedup
 
-[Sentieon Dedup](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/#remove-or-mark-duplicates) is the algorithm used by Sentieon's driver to remove duplicate reads. Only reads aligned by Sentieon's implementation of bwa are processed by this algorithm.
+[Sentieon Dedup](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/#remove-or-mark-duplicates) is the algorithm used by Sentieon's driver to remove duplicate reads. Only reads aligned by Sentieon's implementation of bwa are processed by this algorithm. By default, alignment files are published in bam format. If you would like to store cram files instead, set `--save_mapped_as_cram` to true.
 
 <details markdown="1">
 <summary>Output files from Alignment</summary>
 
 - `{outputdir}/alignment/`
-  - `*.bam`: Bam file containing report containing quality metrics.
-  - `*.bai`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
+  - `*.bam|*.cram`: Alignment file in bam/cram format.
+  - `*.bai|*.crai`: Index of the corresponding bam/cram file.
   - `*.txt`: Text file containing the dedup metrics.
   </details>
 

main.nf

@@ -33,8 +33,6 @@ params.intervals_wgs                  = WorkflowMain.getGenomeAttribute(params,
 params.intervals_y                    = WorkflowMain.getGenomeAttribute(params, 'intervals_y')
 params.known_dbsnp                    = WorkflowMain.getGenomeAttribute(params, 'known_dbsnp')
 params.known_dbsnp_tbi                = WorkflowMain.getGenomeAttribute(params, 'known_dbsnp_tbi')
-params.known_indels                   = WorkflowMain.getGenomeAttribute(params, 'known_indels')
-params.known_mills                    = WorkflowMain.getGenomeAttribute(params, 'known_mills')
 params.ml_model                       = WorkflowMain.getGenomeAttribute(params, 'ml_model')
 params.mt_fasta                       = WorkflowMain.getGenomeAttribute(params, 'mt_fasta')
 params.ploidy_model                   = WorkflowMain.getGenomeAttribute(params, 'ploidy_model')