bump: Update Sawfish to v2.1 (#255)

* bump: Update Sawfish to v2.1
  - add sv_copynum_summary output
  - correct bedgraph->bigWig in parameter_meta.
* bump: Update to Sawfish 2.1.1

Author: williamrowell

docs/family.md

@@ -228,6 +228,7 @@ The `Sample` struct contains sample specific data and metadata. The struct has t
 | Array\[File\] | sv_depth_bw | CNV depth BigWig |  |
 | Array\[File\] | sv_gc_bias_corrected_depth_bw | CNV GC-bias corrected depth BigWig |  |
 | Array\[File\] | sv_maf_bw | CNV MAF BigWig |  |
+| Array\[String\] | sv_copynum_summary | CNV copy number summary JSON |  |
 | Array\[File\] | bcftools_roh_out | ROH calling |  `bcftools roh` |
 | Array\[File\] | bcftools_roh_bed | Generated from above, without filtering |  |
 | File? | joint_sv_vcf | Joint-called structural variant VCF |  |

docs/singleton.md

@@ -182,6 +182,7 @@ flowchart TD
 | File | sv_depth_bw | CNV depth BigWig |  |
 | File | sv_gc_bias_corrected_depth_bw | CNV GC-bias corrected depth BigWig |  |
 | File | sv_maf_bw | CNV MAF BigWig |  |
+| File | sv_copynum_summary | CNV copy number summary JSON |  |
 | File | bcftools_roh_out | ROH calling |  `bcftools roh` |
 | File | bcftools_roh_bed | Generated from above, without filtering |  |
 

docs/tools_containers.md

@@ -13,7 +13,7 @@ We directly use `deepvariant`, `deepvariant-gpu`, `pharmcat`, and `glnexus` cont
 | pb_wdl_base | <ul><li>htslib 1.20</li><li>bcftools 1.20</li><li>samtools 1.20</li><li>bedtools 2.31.0</li><li>python3.9</li><li>numpy 1.24.24</li><li>pandas 2.0.3</li><li>matplotlib 3.7.5</li><li>seaborn 0.13.2</li><li>pysam 0.22.1</li><li>vcfpy 0.13.8</li><li>biopython 1.83</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/6b13cc246dd44e41903d17a660bb5432cdd18dbe/docker/pb_wdl_base) | [sha256:4b889a1f21a6a7fecf18820613cf610103966a93218de772caba126ab70a8e87](https://quay.io/repository/pacbio/pb_wdl_base/manifest/pb_wdl_base@sha256:4b889a1f21a6a7fecf18820613cf610103966a93218de772caba126ab70a8e87) |
 | pbmm2 | <ul><li>pbmm2 1.17.0</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/9591749da92ca57f7283ca1c2268789c45fa341d/docker/pbmm2) | [pbmm2@sha256:5f3f4d1f5dbea5cd4c388ee26b2fecbbb7dbcef449343633e039dca3d3725859](https://quay.io/repository/pacbio/pbmm2/manifest/sha256:5f3f4d1f5dbea5cd4c388ee26b2fecbbb7dbcef449343633e039dca3d3725859) |
 | mosdepth | <ul><li>mosdepth 0.3.9</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/fa84fbf582738c05c750e667ff43d11552ad4183/docker/mosdepth) | [mosdepth@sha256:63f7a5d1a4a17b71e66d755d3301a951e50f6b63777d34dab3ee9e182fd7acb1](https://quay.io/repository/pacbio/mosdepth/manifest/sha256:63f7a5d1a4a17b71e66d755d3301a951e50f6b63777d34dab3ee9e182fd7acb1) |
-| sawfish | <ul><li>sawfish 2.0.4</li><li>sawshark 0.3.0</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/89365e2597635ffbe53870693ec2e047973d0724/docker/sawfish) | [sawfish@sha256:842fcae0ebaf2ab060f1d24512dccd45f9c30d49a609794dfdc4693b4e88dec2](https://quay.io/repository/pacbio/sawfish/manifest/sha256:842fcae0ebaf2ab060f1d24512dccd45f9c30d49a609794dfdc4693b4e88dec2) |
+| sawfish | <ul><li>sawfish 2.1.1</li><li>sawshark 0.3.0</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/72d42592a8d02f98f6f3b50a92d5a0aa4101fc75/docker/sawfish) | [sawfish@sha256:aa764cb24fe9e96af7f3d7ec625fd6b52f02e9f295a3e82ef586d6a5e5351f34](https://quay.io/repository/pacbio/sawfish/manifest/sha256:aa764cb24fe9e96af7f3d7ec625fd6b52f02e9f295a3e82ef586d6a5e5351f34) |
 | trgt | <ul><li>trgt 4.0.0</li><li>`/opt/scripts/check_trgt_coverage.py` 0.1.0</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/c5614951abe48eab926a5246ffb843b4f7816d47/docker/trgt) | [trgt@sha256:7511072d0f57396b1b99c7e0c08934db417138b6b4ce5d93c4974115faab2a0d](https://quay.io/repository/pacbio/trgt/manifest/sha256:7511072d0f57396b1b99c7e0c08934db417138b6b4ce5d93c4974115faab2a0d) |
 | hiphase | <ul><li>hiphase 1.5.0</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/69039c010ada793bab4d38a9bd17a30562b9b671/docker/hiphase) | [hiphase@sha256:353b4ffdae4281bdd5daf5a73ea3bb26ea742ef2c36e9980cb1f1ed524a07482](https://quay.io/repository/pacbio/hiphase/manifest/sha256:353b4ffdae4281bdd5daf5a73ea3bb26ea742ef2c36e9980cb1f1ed524a07482) |
 | mitorsaw | <ul><li>mitorsaw 0.2.4</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/6f6cf280c8ac0b76dd1d08bd830347b0b8ca9cea/docker/mitorsaw) | [mitorsaw@sha256:d0e47fb84e6e962f01a754d1052a24e550694646c0d4afb056c0e3fd7ace7a0d](https://quay.io/repository/pacbio/mitorsaw/manifest/sha256:d0e47fb84e6e962f01a754d1052a24e550694646c0d4afb056c0e3fd7ace7a0d) |

image_manifest.txt

@@ -9,7 +9,7 @@ quay.io/pacbio/pbmm2@sha256:5f3f4d1f5dbea5cd4c388ee26b2fecbbb7dbcef449343633e039
 quay.io/pacbio/pbstarphase@sha256:7daaad3b617a3b8b5914ab0893ee7cc545fd2025a35619211a5b8e25e4c36ac4
 quay.io/pacbio/pbtk@sha256:67cd438ed9f343f90f058108170ddbff8fb1d9b5c193f4016be42b737ee2e73c
 quay.io/pacbio/pb_wdl_base@sha256:4b889a1f21a6a7fecf18820613cf610103966a93218de772caba126ab70a8e87
-quay.io/pacbio/sawfish@sha256:842fcae0ebaf2ab060f1d24512dccd45f9c30d49a609794dfdc4693b4e88dec2
+quay.io/pacbio/sawfish@sha256:aa764cb24fe9e96af7f3d7ec625fd6b52f02e9f295a3e82ef586d6a5e5351f34
 quay.io/pacbio/slivar@sha256:f71a27f756e2d69ec30949cbea97c54abbafde757562a98ef965f21a28aa8eaa
 quay.io/pacbio/svpack@sha256:628e9851e425ed8044a907d33de04043d1ef02d4d2b2667cf2e9a389bb011eba
 quay.io/pacbio/trgt@sha256:7511072d0f57396b1b99c7e0c08934db417138b6b4ce5d93c4974115faab2a0d