run tabix if vcf index is missing in gridss

Add picard dedup

Co-authored-by: Davy Cats <davycats.dc@gmail.com>

Add format parameter to macs2

Speed up integration testing.

Squashed commit of the following:

commit 7fa743cc028b8e2c86bde49244834ee13c13e95b
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 12:34:33 2022 +0100

    Add comment about activate environment

commit 2de7802e03f90cd6e26b3d8287fcb0c6b8b81d11
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 12:26:38 2022 +0100

    Invalidate cache

commit 8ca394d41361acf2511249e3e29688baf0705004
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 12:26:27 2022 +0100

    Consolidate steps

commit 31d09c6f0e86d4625bfa3a6e94a7ced910c7410c
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 11:27:53 2022 +0100

    Use correct path for caching

commit 7e1374ed323bb38d674da09d7270def4a2192d00
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 11:22:10 2022 +0100

    Do not cache conda packages

commit deffd8a0776e15a4df58a1398fcbcb8b0f1430f0
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 11:20:59 2022 +0100

    Remove unnecessary whitespace

commit 8e97bcd4dfd8ee459a23f1931465875c0a41fd49
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 11:20:03 2022 +0100

    Remove debugging task

commit 8338cd4b843245d781d7028f1f1acad45c8c7d0d
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 11:17:18 2022 +0100

    Try to change path

commit 6a75baa36eee340d7a6d766c89163e960a6203b0
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 11:12:18 2022 +0100

    Delete path line in current github env

commit cbbb9fe67cb796a010c01760ca2e05986f979ced
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 11:05:50 2022 +0100

    Properly activate

commit 671568b7c8d79a5141429068a32b72814110b361
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 10:59:46 2022 +0100

    Also printenv

commit 4c8945e8d5305753482538389ddc8af892f493f9
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 10:56:45 2022 +0100

    Manual activate

commit a925c53a99836e81eb0e2b21075356370906c641
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 10:53:10 2022 +0100

    Reset cache number

commit 645ed2b4504d067ea1b26a0922943ef3d5c34622
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 10:51:09 2022 +0100

    Activate environment path

commit 5852d29fb538b80f06a738677e7ae271c6c57fa3
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 10:31:07 2022 +0100

    Proper setting for cache

commit 83f14a939d662d628ca47dc7b82bbc114f164541
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 10:03:45 2022 +0100

    List environments

commit 59267fbba267c0b1726733e390ff471d7012cefa
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 10:01:58 2022 +0100

    Activate environment manually

commit 0a4d2cd5644407308fcc78356a8aef55de86c0c6
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 09:57:32 2022 +0100

    List environments

commit 0bc8fa939eb35a6eb352bb58b1235efecd34056f
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 09:52:02 2022 +0100

    Add mambaforge comment

commit 719d92a0b5245be891d1b5c0eb38d8048abdc5a1
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 09:44:18 2022 +0100

    Use normal conda, since environment is cached

commit e5efbb75109f40cfa8b7b33280ec9707a31970d1
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 09:38:21 2022 +0100

    Also cache environments.txt

commit 4fa66afb6606ceeb7be577df9f20704d96fc3af0
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Fri Feb 11 09:34:46 2022 +0100

    Check home

commit 2ac42e42
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 17:00:27 2022 +0100

    Add an annoying but effective manual check

commit 78d88eae
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 16:54:29 2022 +0100

    Cache correct path

commit c05c9456
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 16:45:51 2022 +0100

    Rename workflow

commit 1c67f010
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 16:45:05 2022 +0100

    Use correct quotes

commit 7f9d2e55
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 16:42:25 2022 +0100

    Only check changed wdl files

commit 0e2a15b3
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 16:34:35 2022 +0100

    remove v parameter

commit 89348dde
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 16:19:02 2022 +0100

    Remove newline

commit 752b8cb4
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 16:17:33 2022 +0100

    Git fetch develop

commit 9216a3f8
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 15:53:13 2022 +0100

    Specifically check origin

commit b54c140d
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 15:44:50 2022 +0100

    Only chek files that are different from the base with womtool validate

commit d9638187
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 15:33:50 2022 +0100

    Correctly use data

commit 8113bfdd
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 15:32:48 2022 +0100

    Set correct env cache param

commit 4f7af2ed
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 15:30:23 2022 +0100

    Add lint-evnironment

commit b026b5a8
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 15:28:50 2022 +0100

    Use mamba env update

commit 41fda1a9
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 15:25:21 2022 +0100

    Use cache

commit fd1a6426
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 14:31:17 2022 +0100

    Add missing done statement

commit 4a64eb43
Merge: a36a2274 f234b0e8
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 14:23:48 2022 +0100

    Merge branch 'develop' into BIOWDL-583

commit a36a2274
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 14:23:26 2022 +0100

    Implement all checks in lint.yml directly

commit 391bb0de
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Wed Feb 9 14:11:33 2022 +0100

    Use a separate lint file

commit 832a131c
Author: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date:   Tue Dec 14 16:32:30 2021 +0100

    Use mamba-forge and mamba to install dependencies

Updates for WGSinCancerDiagnostics