From 96c9a8880a690d2d8058663a805c3b363e416a8d Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Wed, 9 Feb 2022 12:13:59 +1100 Subject: don't strip store paths from bams Due to BAM compression attempting to strip store paths is a waste of time. --- tools/bowtie-align.nix | 1 + tools/bwa-mem.nix | 1 + tools/bwa-mem2.nix | 1 + tools/gridss-assemble.nix | 1 + tools/gridss-softClipsToSplitReads.nix | 1 + tools/hisat2-align.nix | 1 + tools/minimap2-align.nix | 1 + tools/snap-align.nix | 1 + tools/star-align.nix | 1 + tools/subread-align.nix | 1 + tools/whisper-align.nix | 1 + 11 files changed, 11 insertions(+) (limited to 'tools') diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix index cca12a2..d8c0dc5 100644 --- a/tools/bowtie-align.nix +++ b/tools/bowtie-align.nix @@ -38,4 +38,5 @@ stage { ''; passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; }; passthru.multicore = true; + stripStorePaths = !bamOutput; } diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix index 84038d9..6cefc57 100644 --- a/tools/bwa-mem.nix +++ b/tools/bwa-mem.nix @@ -39,4 +39,5 @@ stage { ''; passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; }; passthru.multicore = true; + stripStorePaths = !bamOutput; } diff --git a/tools/bwa-mem2.nix b/tools/bwa-mem2.nix index e6237f0..1c98167 100644 --- a/tools/bwa-mem2.nix +++ b/tools/bwa-mem2.nix @@ -40,4 +40,5 @@ stage { ''; passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; }; passthru.multicore = true; + stripStorePaths = !bamOutput; } diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix index 15e5ca6..56c318f 100644 --- a/tools/gridss-assemble.nix +++ b/tools/gridss-assemble.nix @@ -72,4 +72,5 @@ stage rec { ''; passthru.filetype = filetype.bam { inherit ref; sorting = sort.none { }; }; passthru.multicore = true; + stripStorePaths = false; } diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index ef53322..ac87178 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -40,4 +40,5 @@ stage rec { ''; passthru.filetype = filetype.bam { inherit ref; sorting = sort.none { }; }; passthru.multicore = true; + stripStorePaths = false; } diff --git a/tools/hisat2-align.nix b/tools/hisat2-align.nix index 0a1eb25..736d848 100644 --- a/tools/hisat2-align.nix +++ b/tools/hisat2-align.nix @@ -36,4 +36,5 @@ stage { ''; passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; }; passthru.multicore = true; + stripStorePaths = !bamOutput; } diff --git a/tools/minimap2-align.nix b/tools/minimap2-align.nix index e7e71c6..fdb62cf 100644 --- a/tools/minimap2-align.nix +++ b/tools/minimap2-align.nix @@ -37,4 +37,5 @@ stage { ''; passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.none { }; }; passthru.multicore = true; + stripStorePaths = false; } diff --git a/tools/snap-align.nix b/tools/snap-align.nix index f0bcb21..dca3e9f 100644 --- a/tools/snap-align.nix +++ b/tools/snap-align.nix @@ -35,4 +35,5 @@ stage { ''; passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; }; passthru.multicore = true; + stripStorePaths = false; } diff --git a/tools/star-align.nix b/tools/star-align.nix index 670c6bf..160b65e 100644 --- a/tools/star-align.nix +++ b/tools/star-align.nix @@ -36,4 +36,5 @@ stage { ''; passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; }; passthru.multicore = true; + stripStorePaths = false; } diff --git a/tools/subread-align.nix b/tools/subread-align.nix index 0b0f4c1..ede2d6d 100644 --- a/tools/subread-align.nix +++ b/tools/subread-align.nix @@ -35,4 +35,5 @@ stage { ''; passthru.filetype = filetype.bam { inherit ref; sorting = sort.none { }; }; passthru.multicore = true; + stripStorePaths = false; } diff --git a/tools/whisper-align.nix b/tools/whisper-align.nix index 19eef0d..e76e921 100644 --- a/tools/whisper-align.nix +++ b/tools/whisper-align.nix @@ -37,4 +37,5 @@ stage { ''; passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; }; passthru.multicore = true; + stripStorePaths = false; } -- cgit v1.2.3