From 8ecadc3e3837a12802474291fdaaed83e1b32659 Mon Sep 17 00:00:00 2001 From: borauyar Date: Thu, 19 Apr 2018 16:19:14 +0200 Subject: [PATCH] add samtools stats rule - connect with multiqc --- dag.pdf | Bin 20065 -> 22438 bytes pigx_crispr.py | 17 ++++++++++++++--- 2 files changed, 14 insertions(+), 3 deletions(-) diff --git a/dag.pdf b/dag.pdf index 06b63a69977e32649b9927b4f2b20e1799ab4670..23e749b4cfc6414cfaa924dcb3eda21b0cdb79b3 100644 GIT binary patch delta 20917 zcmV)9K*hh|oB^h<0gz08?OfZgB*|5M&#$P*?uRbN{o*$cAS6p5F!N?v*0^TI2KBMW zHVF88)>=CvGV9c_UE?au7%{Cmxg#p$n)|+Y#BVl#;=kYi;`Dmp>(e)zJLi(p$(>uqpO{WR{<~8+{RiIs5nBK2_LHBY+MT|C+Ppjc{V7C$&L{7~ z>Gc5n;BKG`{-#;$8X;E}J_f*k z7ia*7U(mLG=VYxLE?{5k<@C?mM8{2i`C{wm-h0hORjc5A!TX(!zIfe!@XaUp35z^^ z@y+&=4_|+b{=wj)f+NPdtFuj*rW! zVQX2g?t}(>gr;f%eE7o0#;4VLXRWLgR_dt%#@`E`jir!(__`i!4nQ5T0^N^?>N&g` zxjEJQzEA5wtNz~C`EqUe=Y5B24n6tPEkIf!y0~_#z?Gay7O9-8_dq|4M$GHy)+&ps z^i#;ua5S}Wb}62cKPS{}wE&~D$I{N8GtB*5Ba!qRUAATY{&`@ne|VPcPP3`!+AC(+ 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"{sample}.mpileup.counts.tsv") @@ -142,7 +152,8 @@ def get_output_file_list(DIR, ext): rule multiqc: input: fastqc = get_output_file_list(FASTQC_DIR, "fastqc.done"), - trimmomatic = get_output_file_list(TRIMMED_READS_DIR, "fastq.gz") + trimmomatic = get_output_file_list(TRIMMED_READS_DIR, "fastq.gz"), + samtools = get_output_file_list(MAPPED_READS_DIR, "samtools.stats.txt") output: os.path.join(OUTPUT_DIR, "multiqc", "multiqc_report.html") params: