From ef2d9e9d3523d71b0e7a236fc94d80c5867f6e52 Mon Sep 17 00:00:00 2001
From: james94 <james94@mi.fu-berlin.de>
Date: Wed, 10 Mar 2021 22:38:26 +0100
Subject: [PATCH] new merq naming
---
.DS_Store | Bin 18436 -> 16388 bytes
programs/.DS_Store | Bin 6148 -> 6148 bytes
rules/rulesNew.smk | 16 ++++++++--------
3 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/.DS_Store b/.DS_Store
index 5b72387d5cbba55edf7bad03f3912bd1c763ac59..b772272316d68012d461a11782678cd6932c77f3 100644
GIT binary patch
delta 393
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z!ZMkgMN*(FxF|0tKQA4mnSp_Ubuy2DEaRKWd$f!;3v!6DY;1VT#L3721{~aAq0MSM
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REtAuEdN+5Pu3^Gs0RZ)`W_SPq
delta 945
zcmZo^U~HMdsKUU&!01$(V#vVYz`(%3!2qEJco-O1xEL4|co-NAcqXc7Gx|;pFyE}e
z*uXs5z=maFx8!C{-CQO{*2xRa#hDm4ZuZfRWaI&v#Q+8z+?xd%#aTA1^E_demt<gI
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FGXQgo@4f&4
diff --git a/programs/.DS_Store b/programs/.DS_Store
index 54b7e113f4461e5b893542b74cd8285135498795..62cf363b4ffd08bcddfc2d41efafcdf2186d7794 100644
GIT binary patch
delta 87
zcmZoMXfc=|#>B)qu~2NHo}wrR0|Nsi1A_nqLn%WMLnVVQgCT?7#=_-{j2x5aux#G^
ogjJboV}mO5W_AvK4kjkf&4L`?nJ4p$ID#~Sbh2!Y5Lv?v063`<e*gdg
delta 376
zcmZoMXfc=|#>B!ku~2NHo}wr}0|Nsi1A_nqLn%WMLuF37VQ_N(=0xV@%=I8Cc7|Mr
zRE8pkLS*UO0tN&?Q<0nR;*yk;pTxkx!11s1tI^U=ha4Fg7%)_&5L6|^P+5=xat*?|
z$vjM(>jhAq#1PNm#ZbzS$B@ck#9#ozDaFY-N%{FXAU6_J4Dm433ir%I44|+;@iUqQ
wLPiV*DDLvwuz5F=I@4x$4t@?M7Ou^S%-@+O^NTogFfuSOf!we;LSzjy0NpZFA^-pY
diff --git a/rules/rulesNew.smk b/rules/rulesNew.smk
index 3485800..230f47d 100644
--- a/rules/rulesNew.smk
+++ b/rules/rulesNew.smk
@@ -239,8 +239,8 @@ rule merqury:
workflow.cores * 0.5
output:
report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.qv"), caption="../report/merqury/qvScore.rst", category="QV Estimate", subcategory="{sample}"),
- report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.st.png"), caption="../report/merqury/spectra-cn_stacked.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
- report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.fl.png"), caption="../report/merqury/spectra-cn_filled.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
+ report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png"), caption="../report/merqury/spectra-cn_stacked.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
+ report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"), caption="../report/merqury/spectra-cn_filled.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist")
log:
os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/{sample}_merqury.log")
@@ -268,8 +268,8 @@ rule merqury:
rule genomescope2:
input:
hist=os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist"),
- check1=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.fl.png"),
- check2=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.st.png")
+ check1=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
+ check2=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png")
params:
outFolder=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/"),
cpHist=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_dB.21.histo")
@@ -347,8 +347,8 @@ rule saveConfiguration_and_getKeyValues:
gscopeLin=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_linear_plot.png"),
busco=os.path.join(config['Results'], "{sample}" + "/1_busco5/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"),
qv=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.qv"),
- spectraStacked=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.st.png"),
- spectraFlat=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.fl.png"),
+ spectraStacked=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png"),
+ spectraFlat=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
# os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_merqury.log"),
# os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"),
scaffStats=os.path.join(config['Results'],"{sample}" + "/4_assemblyStats/{sample}_scaffold_stats.tsv"),
@@ -372,8 +372,8 @@ rule saveConfiguration_and_getKeyValues:
gscopeLin=os.path.join(config['Results'], "{sample}" +"/5_Key_Results/" + "{sample}" + "_gScope_linear_plot.png"),
busco=os.path.join(config['Results'], "{sample}" + "/5_Key_Results/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"),
qv=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.qv"),
- spectraStacked=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.spectra-cn.st.png"),
- spectraFlat=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.spectra-cn.fl.png"),
+ spectraStacked=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png"),
+ spectraFlat=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
# os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_merqury.log"),
# os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"),
scaffStats=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/{sample}_scaffold_stats.tsv"),
--
GitLab