From eaa8851208b8bec85d2d3f9e7bfee89772b4d3ab Mon Sep 17 00:00:00 2001 From: Ksenia Date: Thu, 5 Sep 2024 13:28:52 +0100 Subject: [PATCH] Update usage.md Update test yaml --- docs/usage.md | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 83b5649..c121091 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -59,20 +59,27 @@ Example is based on [test.yaml](../assets/test.yaml). dataset: id: baUndUnlc1 illumina_10X: - reads: /lustre/scratch123/tol/resources/nextflow/test-data/Undibacterium_unclassified/genomic_data/baUndUnlc1/10x/ + reads: + - https://tolit.cog.sanger.ac.uk/test-data/Undibacterium_unclassified/genomic_data/baUndUnlc1/10x/baUndUnlc1_S12_L002_R1_001.fastq.gz + - https://tolit.cog.sanger.ac.uk/test-data/Undibacterium_unclassified/genomic_data/baUndUnlc1/10x/baUndUnlc1_S12_L002_R2_001.fastq.gz + - https://tolit.cog.sanger.ac.uk/test-data/Undibacterium_unclassified/genomic_data/baUndUnlc1/10x/baUndUnlc1_S12_L002_I1_001.fastq.gz pacbio: reads: - - reads: /lustre/scratch123/tol/resources/nextflow/test-data/Undibacterium_unclassified/genomic_data/baUndUnlc1/pacbio/fasta/HiFi.reads.fasta + - reads: https://tolit.cog.sanger.ac.uk/test-data/Undibacterium_unclassified/genomic_data/baUndUnlc1/pacbio/fasta/HiFi.reads.fasta HiC: reads: - - reads: /lustre/scratch123/tol/resources/nextflow/test-data/Undibacterium_unclassified/genomic_data/baUndUnlc1/hic-arima2/41741_2#7.sub.cram + - reads: https://tolit.cog.sanger.ac.uk/test-data/Undibacterium_unclassified/genomic_data/baUndUnlc1/hic-arima2/41741_2%237.sub.cram hic_motif: GATC,GANTC,CTNAG,TTAA +hic_aligner: bwamem2 busco: lineage: bacteria_odb10 mito: species: Caradrina clavipalpis min_length: 15000 code: 5 + fam: https://github.com/c-zhou/OatkDB/raw/main/v20230921/insecta_mito.fam +plastid: + fam: https://github.com/c-zhou/OatkDB/raw/main/v20230921/acrogymnospermae_pltd.fam ```