Closed FelixKrueger closed 4 years ago
I have now updated the YAML report to include some Metadata (as requested here: https://github.com/ewels/MultiQC/pull/593#issuecomment-557804044). A sample YAML report now looks like this:
---
Meta:
tool: SNPsplit
version: 0.3.4_dev
infile: lane4904.hicup.bam
date_run: Mon Nov 25 15:37:32 2019
mode: Hi-C
library: paired-end
command: SNPsplit --snp all_SNPs_CAST_EiJ_GRCm38.txt.gz lane4904.hicup.bam --hic
Tagging:
total_reads: 1616940
unaligned: 0
percent_unaligned: 0.00
g1: 391351
percent_g1: 24.20
g2: 358019
percent_g2: 22.14
unassignable: 864197
percent_unassignable: 53.45
no_snp: 2407
percent_no_snp: 0.15
bizarre: 3373
percent_bizarre: 0.21
SNP_annotation: all_SNPs_CAST_EiJ_GRCm38.txt.gz
SNPs_stored: 20668547
N_containing_reads: 754253
non_N_containing_reads: 861790
N_deletion: 897
percent_N_deletion: 0.06
multi_N_deletion: 1
N_was_known_SNP: 1430442
percent_N_was_known_SNP: 99.97
N_not_known: 466
percent_N_not_known: 0.03
Sorting:
tagged_infile: lane4904.hicup.allele_flagged.bam
HiC_total_pairs: 808470
HiC_unassignable_UA_UA: 236613
HiC_percent_unassignable_UA_UA: 29.27
HiC_genome1_G1_G1: 89316
HiC_percent_genome1_G1_G1: 11.05
HiC_genome2_G2_G2: 81093
HiC_percent_genome2_G2_G2: 10.03
HiC_G1_UA_total: 203114
HiC_percent_G1_UA_total: 25.12
HiC_G1_UA: 101727
HiC_UA_G1: 101387
HiC_G2_UA_total: 186113
HiC_percent_G2_UA_total: 23.02
HiC_G2_UA: 92750
HiC_UA_G2: 93363
HiC_G1_G2_total: 8855
HiC_percent_G1_G2_total: 1.10
HiC_G1_G2: 4391
HiC_G2_G1: 4464
HiC_conflicting: 3366
HiC_percent_conflicting: 0.42
...
YAML-wise this seems to be good enough for the moment.
Phil asked if we could produce the stats in YAML format to make it easier to integrate into MultiQC https://github.com/ewels/MultiQC/pull/593#issuecomment-555764517