Merge pull request #27 from clinical-genomics-uppsala/multiqc_tot_reads

fix: Multiqc tot reads

config/config.yaml

@@ -13,7 +13,7 @@ modules:
   snv_indels: "v0.5.0"
   qc: "ca947b1"
 
-default_container: "docker://hydragenetics/common:0.4.0"
+default_container: "docker://hydragenetics/common:1.8.1"
 
 reference:
   fasta: "/data/ref_genomes/GRCh38/reference_grasnatter/homo_sapiens.fasta"

config/multiqc_config.yaml

@@ -91,15 +91,15 @@ table_columns_visible:
     PCT_30X: False
     PCT_TARGET_BASES_30X: False
     FOLD_ENRICHMENT: False
-    TOTAL_READS: True
+    TOTAL_READS: False
   Samtools:
     error_rate: False
     non-primary_alignments: False
     reads_mapped: False
     reads_mapped_percent: True
     reads_properly_paired_percent: True
     reads_MQ0_percent: False
-    raw_total_sequences: False #only on bedfile not total of fastq, bases on target only
+    raw_total_sequences: True #only on bedfile not total of fastq, bases on target only
 
 # Patriks plug in, addera egna columner till general stats
 multiqc_cgs:

docs/result_files.md

@@ -39,8 +39,8 @@ The general statistics table are ordered based on the sample order in `SampleShe
 
 | Column Name | Origin | Comment | 
 | --- | --- | --- |
-| K Reads | [Picard](https://broadinstitute.github.io/picard/) HSMetrics | Total number of reads in inputfile (`alignment/samtools_merge_bam/{sample}_{type}.bam`) |
-| % Mapped| [Samtools stats](http://www.htslib.org/doc/samtools-stats.html) | Only reads on target (`config[reference][design_bed]`) |
+| K Reads | [Samtools stats](http://www.htslib.org/doc/samtools-stats.html)  | Total number of reads in inputfile (`alignment/samtools_merge_bam/{sample}_{type}.bam`) |
+| % Mapped| [Samtools stats](http://www.htslib.org/doc/samtools-stats.html) | Percent reads mapped, anywhere in the reference (no design file used) |
 | % Proper pairs| [Samtools stats](http://www.htslib.org/doc/samtools-stats.html) | Only reads on target (`config[reference][design_bed]`) |
 | Average Quality | [Samtools stats](http://www.htslib.org/doc/samtools-stats.html) | Ratio between sum of base quality over total length. Only reads on target (`config[reference][design_bed]`) |
 | Median | [Mosdepth](https://github.com/brentp/mosdepth) | Median Coverage over coding exon in design (`config[reference][exon_bed]`) |

docs/steps.md

@@ -3,7 +3,7 @@ To go into details of the pipeline we dived the pipeline into modules similar to
 
 ---
 ## Prealignment
-See the **Prealignment** hydra-genetics module documentation on [ReadTheDoc](https://hydra-genetics-prealignment.readthedocs.io/en/latest/) or [github]() documentation for more details on the softwares. Default hydra-genetics settings/resources are used if no configuration is specified.
+See the **Prealignment** hydra-genetics module documentation on [ReadTheDoc](https://hydra-genetics-prealignment.readthedocs.io/en/latest/) or [github](https://github.com/hydra-genetics/prealignment) documentation for more details on the softwares. Default hydra-genetics settings/resources are used if no configuration is specified.
 
 ![dag plot](includes/images/prealignment.png){: style="height:30%;width:30%"}
 
@@ -87,7 +87,7 @@ Variants are called using [**Parabricks deepvariant** v4.1.1-1](https://docs.nvi
 The standard vcf files is decomposed with [**vt decompose**](https://genome.sph.umich.edu/wiki/Vt#Decompose) followed by [**vt decompose_blocksub**](https://genome.sph.umich.edu/wiki/Vt#Decompose_biallelic_block_substitutions) v2015.11.10. The decomposed vcf files are then normalized by [**vt normalize**](https://genome.sph.umich.edu/wiki/Vt#Normalization) v2015.11.10.
 
 ### Annotation
-Both the normalized standard VCF files and the genome vcf files are then annotated using **[VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)** v109. Vep is run with the extra parameters `--assembly GRCh38 --check_existing --pick --variant_class --everything`.
+Both the normalized standard VCF files and the genome vcf files are then annotated using **[VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)** v109.3. Vep is run with the extra parameters `--assembly GRCh38 --check_existing --pick --variant_class --everything`.
 
 See the [annotation hydra-genetics module](https://hydra-genetics-annotation.readthedocs.io/en/latest/) for additional information.
 
@@ -139,7 +139,7 @@ The report is configured based on a MultiQC config file.
 **[Mosdepth](https://github.com/brentp/mosdepth)** v0.3.2 is used together with a bedfile covering all coding exons (`config[reference][exon_bed]`) and thresholds (`10,20,50`) to calculate coverage.
 
 ### Samtools
-**[Samtools stats](http://www.htslib.org/doc/samtools-stats.html)** v1.15 is run on BWA-mem aligned and merged bam files over the full bedfile (`config[reference][design_bed]`).
+**[Samtools stats](http://www.htslib.org/doc/samtools-stats.html)** v1.15 is run on BWA-mem aligned and merged bam files without any designfile.
 
 ### Picard
 **[Picard](https://broadinstitute.github.io/picard/)** v2.25.4 is run on BWA-mem aligned and merged bam files collecting a number of metrics. The metrics calculated are listed below:

workflow/Snakefile

@@ -235,6 +235,11 @@ use rule picard_collect_multiple_metrics from qc as qc_picard_collect_multiple_m
         extra=lambda wildcards, input: f" INTERVALS={input.intervals}",
 
 
+use rule samtools_stats from qc as qc_samtools_stats with:
+    params:
+        extra="%s " % (config.get("samtools_stats", {}).get("extra", ""),),
+
+
 use rule multiqc from qc as qc_multiqc with:
     input:
         files=lambda wildcards: set(