From dfca569f1bdeeb8db9082812f36acc1847d1cea2 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 19 May 2020 14:36:58 -0400 Subject: [PATCH 1/2] impose a minimum contig length for spades --- pipes/WDL/workflows/classify_multi.wdl | 1 + 1 file changed, 1 insertion(+) diff --git a/pipes/WDL/workflows/classify_multi.wdl b/pipes/WDL/workflows/classify_multi.wdl index a7dd71ea2..72d3b1b99 100644 --- a/pipes/WDL/workflows/classify_multi.wdl +++ b/pipes/WDL/workflows/classify_multi.wdl @@ -112,6 +112,7 @@ workflow classify_multi { assembler = "spades", reads_unmapped_bam = rmdup_ubam.dedup_bam, trim_clip_db = trim_clip_db, + spades_min_contig_len = 800, always_succeed = true } if(defined(blast_db_tgz) && defined(krona_taxonomy_db_blast_tgz)) { From a9e8f98a78e57bae75fcf313a5feb0249d14ef37 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 19 May 2020 14:37:33 -0400 Subject: [PATCH 2/2] switch all default kraken2 databases to custom built one --- pipes/dnax/dx-defaults-classify_kraken2.json | 2 +- pipes/dnax/dx-defaults-classify_multi.json | 2 +- pipes/dnax/dx-defaults-demux_metag.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pipes/dnax/dx-defaults-classify_kraken2.json b/pipes/dnax/dx-defaults-classify_kraken2.json index 5925c4bbc..57ae3639f 100644 --- a/pipes/dnax/dx-defaults-classify_kraken2.json +++ b/pipes/dnax/dx-defaults-classify_kraken2.json @@ -1,6 +1,6 @@ { "classify_kraken2.kraken2.kraken2_db_tgz": - "dx://file-Fpp4V6j0xf5bYPKQ5J13JVyj", + "dx://file-Fq1ZPzQ0GY2bkq6K8KKk82G3", "classify_kraken2.kraken2.krona_taxonomy_db_tgz": "dx://file-Fpp14j00xf5Xjq665v8v93z8" } diff --git a/pipes/dnax/dx-defaults-classify_multi.json b/pipes/dnax/dx-defaults-classify_multi.json index 02453e5eb..45a991262 100644 --- a/pipes/dnax/dx-defaults-classify_multi.json +++ b/pipes/dnax/dx-defaults-classify_multi.json @@ -6,7 +6,7 @@ "dx://file-BXF0vYQ0QyBF509G9J12g927", "classify_multi.kraken2_db_tgz": - "dx://file-Fpp4V6j0xf5bYPKQ5J13JVyj", + "dx://file-Fq1ZPzQ0GY2bkq6K8KKk82G3", "classify_multi.krona_taxonomy_db_kraken2_tgz": "dx://file-Fpp14j00xf5Xjq665v8v93z8", diff --git a/pipes/dnax/dx-defaults-demux_metag.json b/pipes/dnax/dx-defaults-demux_metag.json index 05e9cd89d..16717a378 100644 --- a/pipes/dnax/dx-defaults-demux_metag.json +++ b/pipes/dnax/dx-defaults-demux_metag.json @@ -11,7 +11,7 @@ "dx://file-BXF0vYQ0QyBF509G9J12g927", "demux_metag.kraken2_db_tgz": - "dx://file-Fpp4V6j0xf5bYPKQ5J13JVyj", + "dx://file-Fq1ZPzQ0GY2bkq6K8KKk82G3", "demux_metag.krona_taxonomy_db_kraken2_tgz": "dx://file-Fpp14j00xf5Xjq665v8v93z8", "demux_metag.blast_db_tgz":