From 2aa7733051270a75c54d4f4688e6daab66306efe Mon Sep 17 00:00:00 2001
From: james94 <james94@mi.fu-berlin.de>
Date: Wed, 10 Mar 2021 20:52:28 +0100
Subject: [PATCH] old history interfering
---
.DS_Store | Bin 18436 -> 18436 bytes
Snakefile | 5 ++++-
programs/.DS_Store | Bin 6148 -> 6148 bytes
rules/rulesNew.smk | 16 ++++++++--------
4 files changed, 12 insertions(+), 9 deletions(-)
diff --git a/.DS_Store b/.DS_Store
index cb5fafc917bf9ff8a64362f5304ef7b671993f20..5b72387d5cbba55edf7bad03f3912bd1c763ac59 100644
GIT binary patch
delta 719
zcmZpfz}PZ@ae@>R3)e&$V@BVJ0p^<(7#o-;8@RAc?3UczsGG|q!OFnEz{*g>P|A?Q
zkjhY;Qk<NVl%Jo&xVh0NnvsWrfq{_$3^=$q3o?qcY*y!CWML}5yje>?l~tpwuu-(^
z&ml)tGjj7&T#|C~lNcBnI3OxEmy1r}s#jrPU|?g=V@PGlWhh`MVW`YWHw;eB&n*C3
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zkS*i(PTpSx@fVUj!XlXbWLpJErtl4$BNXm1F-c2LeyAk3IYil<mF?@%P=$-1Cr{MS
zVLNg>qB;b`RG9o&Ba6{yvY(~|+xZy_C$Ic7IY(0p#_Z9QVJcvlI6-9cKFyDejFUHL
zDX=ibm4BMNK}&S=ORaXM%_5AK85#K|PEg=by!h<&%0Gu3Cr%I(LO2Q`Dl*x_fQN-C
zI{{?g<{Se}MkbER&C?CFS=nBDCI3J1dGZM}IT-VenF8a6#k}T>lO09APfpQLr;+2&
xGfrlA5N2ZG+AQOs!omtlRt=LKU4$n`xGdc)rN_)T`G)B$n4{3$H<{P`JOEI)?gsz>
delta 661
zcmZpfz}PZ@ae@>RL;FM-V@CIh0p^npTv#S^vq(->FyP@3I+}Z7>8C@Ell$1DSr{0%
zEtp)WB|3SEf#hZ(4pEkk4R4t^85zKUgL|_ehZxIdH6A7wrjk3GwFFdIHRNv02Ww|w
zU|?k^Vkl+EVMt{t&dpD8Ny^DjVqjq4fT-A9E;@yaQGW6i1wA>NiN_fj7+4te7}6Os
z8A=K=41<&Na|=M0um&h>R#3dd#3b{6@<KJm&GITHtQ@*A*<d>+FI1D8T&c;!aqi7$
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zjNm}&(dJ=cTzh`zWC0fO&6~AbnKlcv)G<vgk!9qaEWjc%*#kK^K>`H^Jj~D#-8{uW
zlaa|GY4d(VZC1AKK9I8}e=w7SF-6Q37#}P)HD{dsP$Yb^j;8vc_qF6?b_Zc5hW5=e
k4k|2+43lkmq$kI?ES%h~?y@=4w2=|!GjvZ*HZ}ha0LvZI761SM
diff --git a/Snakefile b/Snakefile
index 32dde88..c3d7e49 100644
--- a/Snakefile
+++ b/Snakefile
@@ -99,9 +99,12 @@ else:
# return False
#
+
+print("the number of threads to be used is", max_threads)
+
if "Results" not in config:
config["Results"] = "results"
-max_threads=workflow.cores
+
report: "report/workflow.rst"
include: "rules/rulesNew.smk"
diff --git a/programs/.DS_Store b/programs/.DS_Store
index c4ff712f42ba86cc475a1b61d0ddace2a027f5ee..54b7e113f4461e5b893542b74cd8285135498795 100644
GIT binary patch
delta 463
zcmZoMXfc=|#>B!ku~2NHo}wr}0|Nsi1A_nqLn%WMLuF37VQ_N(=8eqDnd?DP><qaK
zsSHI7g~-ym1q=v)rXn}r#U&{xKZ${Xf#YB2SEHq$4mmO~Fkq-kA*iaJp|T(Y<Qf#~
zxKSO%pvz#$pvPbcaW_<@`$Z`R1_m4|ksWA$^2VN(f4~mJRP78lI5!{RQoPE+s!<&5
zUBEComq}%^0TTx!gcZwVGMSM%g6*yMnJX**Opa$(;eap?IZhU27UM_O&X_h~V_`ev
iW_AvK4ki|^%^R7&Gf(ChapYiRU|<3T|K<phHOv5>(sP0U
delta 190
zcmZoMXfc=|#>B)qu~2NHo}wrx0|Nsi1A_nqLn%WMLnT8zgBL^T#=_-{jGU9#vZ_oj
zVC7(B1heL{nuz4)ySOCf<R>vOFmUXhv$%x&-62Piq)2Xl3O0!vw)LiglAP}*>$9nF
zK$wRdCqHBr<1ffC3{K9^EnooIpM7DoAcq*s#0JOB>>T_YOiY}c1v$PmPv#eK<NzyR
MU|`uCA+m-U0EN&rWB>pF
diff --git a/rules/rulesNew.smk b/rules/rulesNew.smk
index 5f33143..3485800 100644
--- a/rules/rulesNew.smk
+++ b/rules/rulesNew.smk
@@ -228,12 +228,12 @@ rule merqury:
if wildcards.sample in samples.index else '',
merylDB=os.path.join(config['Results'],"{sample}"+ "/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.meryl")
params:
- script = os.path.join(workflow.basedir, "programs/merqury_June2020/merqury.sh"),
+ script = os.path.join(workflow.basedir, "programs/merqury-1.1/merqury.sh"),
outFile= "{sample}" + "_merq",
# outFile= os.path.join(config['Results'], "{sample}" +"/QVstats_merylAndMerqury/{sample}_merq"),
merylPath = os.path.join(workflow.basedir, "programs/meryl-1.0/Linux-amd64/bin:$PATH"),
outPath= os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury"),
- export= os.path.join(workflow.basedir, "programs/merqury_June2020")
+ export= os.path.join(workflow.basedir, "programs/merqury-1.1")
# symlink=os.path.join(config['Results'], "{sample}" + "/{sample}.fasta")
threads:
workflow.cores * 0.5
@@ -243,7 +243,7 @@ rule merqury:
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}"),
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}" + "_merq.spectra-cn.log")
+ os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/{sample}_merqury.log")
priority:
3
conda:
@@ -268,7 +268,8 @@ rule merqury:
rule genomescope2:
input:
hist=os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist"),
- logCheck=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/" + "{sample}" + "_merq.spectra-cn.log")
+ 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")
params:
outFolder=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/"),
cpHist=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_dB.21.histo")
@@ -278,7 +279,7 @@ rule genomescope2:
linearPlot=report(os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_linear_plot.png"), caption="../report/genomescope/linearplot.rst", category="Genomescope Profile", subcategory="{sample}"),
estimatedSize=temp(os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_sizeEst.txt"))
conda:
- "../envs/merylMerq.yaml"
+ "../envs/genomescope.yaml"
shell:
"""
expand -t 1 {input.hist} > {params.cpHist}
@@ -340,7 +341,7 @@ rule assemblyStats:
rule saveConfiguration_and_getKeyValues:
input:
- checkLog=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/" + "{sample}" + "_merq.spectra-cn.log"),
+# checkLog=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/" + "{sample}" + "_merq.spectra-cn.log"),
gscopeSum=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_summary.txt"),
gscopeLog=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_log_plot.png"),
gscopeLin=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_linear_plot.png"),
@@ -362,7 +363,7 @@ rule saveConfiguration_and_getKeyValues:
output:
# newSampleSheet=os.path.join(config['Results'],"{sample}"+ "/keyResults/savedSampleSheet.tsv"),
# newConfigFile=os.path.join(config['Results'],"{sample}"+ "/keyResults/savedConfig.yaml"),
- merqLog=os.path.join(config['Results'],"logs/2_merylAndMerq/" + "{sample}" + "_merqury.spectra-cn.log"),
+# merqLog=os.path.join(config['Results'],"logs/2_merylAndMerq/" + "{sample}" + "_merqury.spectra-cn.log"),
keyValues=temp(os.path.join(config['Results'],"{sample}"+ "/5_Key_Results/aggregate.tsv")),
rowNames=temp(os.path.join(config['Results'],"{sample}"+ "/5_Key_Results/aggregate_rowNames.tsv")),
keyValuesWithRowNames=os.path.join(config['Results'],"{sample}"+ "/5_Key_Results/{sample}_aggregatedResults.tsv"),
@@ -384,7 +385,6 @@ rule saveConfiguration_and_getKeyValues:
"../envs/dos2unix.yaml"
shell:
"""
- cp {input.checkLog} {output.merqLog}
cp {input.gscopeSum} {output.gscopeSum}
cp {input.gscopeLog} {output.gscopeLog}
cp {input.gscopeLin} {output.gscopeLin}
--
GitLab