R markdown integration

tbersez · May 6, 2019 · 7178d24 · 7178d24
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diff --git a/docs/AllMine outputs.rst b/docs/AllMine outputs.rst
@@ -47,3 +47,9 @@ tabular file displaying all non synonymous SNPs found by AllMine. Base and amino
 acid reference and variation are indicated as well as genotype (het or hom),
 location in the gene (exon1, exon2 ...). If a variant is found in more than one
 sample, all concerned samples are indicated in the SAMPLE(s) column.
+
+Run Report
+----------
+
+Allmine build an R markdown report to sum up most of the information about
+the run. This report also include coverage plots for regions of interest. 
diff --git a/docs/_build/doctrees/AllMine outputs.doctree b/docs/_build/doctrees/AllMine outputs.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/html/AllMine outputs.html b/docs/_build/html/AllMine outputs.html
@@ -88,6 +88,7 @@
 <li class="toctree-l2"><a class="reference internal" href="#mapped-reads-and-de-novo-splicing-junctions">Mapped reads and de novo splicing junctions</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#putative-snps">Putative SNPs</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#non-synonymous-variant-summary">Non synonymous variant summary</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#run-report">Run Report</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="Modules documentation.html">Modules documentation</a></li>
@@ -202,6 +203,11 @@ <h2>Non synonymous variant summary<a class="headerlink" href="#non-synonymous-va
 location in the gene (exon1, exon2 …). If a variant is found in more than one
 sample, all concerned samples are indicated in the SAMPLE(s) column.</p>
 </div>
+<div class="section" id="run-report">
+<h2>Run Report<a class="headerlink" href="#run-report" title="Permalink to this headline">¶</a></h2>
+<p>Allmine build an R markdown report to sum up most of the information about
+the run. This report also include coverage plots for regions of interest.</p>
+</div>
 </div>
 
 

diff --git a/docs/_build/html/_sources/AllMine outputs.rst.txt b/docs/_build/html/_sources/AllMine outputs.rst.txt
@@ -47,3 +47,9 @@ tabular file displaying all non synonymous SNPs found by AllMine. Base and amino
 acid reference and variation are indicated as well as genotype (het or hom),
 location in the gene (exon1, exon2 ...). If a variant is found in more than one
 sample, all concerned samples are indicated in the SAMPLE(s) column.
+
+Run Report
+----------
+
+Allmine build an R markdown report to sum up most of the information about
+the run. This report also include coverage plots for regions of interest. 
diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
@@ -180,6 +180,7 @@ <h1>AllMine Documentation<a class="headerlink" href="#allmine-documentation" tit
 <li class="toctree-l2"><a class="reference internal" href="AllMine outputs.html#mapped-reads-and-de-novo-splicing-junctions">Mapped reads and de novo splicing junctions</a></li>
 <li class="toctree-l2"><a class="reference internal" href="AllMine outputs.html#putative-snps">Putative SNPs</a></li>
 <li class="toctree-l2"><a class="reference internal" href="AllMine outputs.html#non-synonymous-variant-summary">Non synonymous variant summary</a></li>
+<li class="toctree-l2"><a class="reference internal" href="AllMine outputs.html#run-report">Run Report</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="Modules documentation.html">Modules documentation</a><ul>

diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
diff --git a/modules/.snakemake/log/2019-01-28T092943.845717.snakemake.log b/modules/.snakemake/log/2019-01-28T092943.845717.snakemake.log
@@ -0,0 +1,3 @@
+NameError in line 10 of /home/aa/pipeline_dev/Allmine/modules/fastp.py:
+name 'wildcards' is not defined
+  File "/home/aa/pipeline_dev/Allmine/modules/fastp.py", line 10, in <module>
diff --git a/modules/.snakemake/log/2019-01-28T093128.728398.snakemake.log b/modules/.snakemake/log/2019-01-28T093128.728398.snakemake.log
@@ -0,0 +1,5 @@
+Building DAG of jobs...
+InputFunctionException in line 8 of /home/aa/pipeline_dev/Allmine/modules/fastp.py:
+KeyError: '{samples}'
+Wildcards:
+samples=ecoA
diff --git a/modules/.snakemake/log/2019-01-28T093338.568260.snakemake.log b/modules/.snakemake/log/2019-01-28T093338.568260.snakemake.log
@@ -0,0 +1,5 @@
+Building DAG of jobs...
+InputFunctionException in line 8 of /home/aa/pipeline_dev/Allmine/modules/fastp.py:
+KeyError: 'R2'
+Wildcards:
+samples=ecoB
diff --git a/modules/.snakemake/log/2019-01-28T093927.259765.snakemake.log b/modules/.snakemake/log/2019-01-28T093927.259765.snakemake.log
@@ -0,0 +1,5 @@
+Building DAG of jobs...
+MissingInputException in line 5 of /home/aa/pipeline_dev/Allmine/modules/fastp.py:
+Missing input files for rule all:
+trimmed/ecoA_1_trim.fastq.gz
+trimmed/ecoA_2_trim.fastq.gz
diff --git a/modules/.snakemake/log/2019-01-28T093950.878805.snakemake.log b/modules/.snakemake/log/2019-01-28T093950.878805.snakemake.log
@@ -0,0 +1,7 @@
+Building DAG of jobs...
+File path /home/aa/pipeline_dev/Allmine/modules//home/aa/pipeline_dev/Allmine/testdata/ecoA_1.fastq contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
+File path /home/aa/pipeline_dev/Allmine/modules//home/aa/pipeline_dev/Allmine/testdata/ecoA_2.fastq contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
+MissingInputException in line 10 of /home/aa/pipeline_dev/Allmine/modules/fastp.py:
+Missing input files for rule run_fastp_paired:
+/home/aa/pipeline_dev/Allmine/modules//home/aa/pipeline_dev/Allmine/testdata/ecoA_1.fastq
+/home/aa/pipeline_dev/Allmine/modules//home/aa/pipeline_dev/Allmine/testdata/ecoA_2.fastq
diff --git a/modules/.snakemake/log/2019-01-28T094058.844762.snakemake.log b/modules/.snakemake/log/2019-01-28T094058.844762.snakemake.log
@@ -0,0 +1,27 @@
+Building DAG of jobs...
+Using shell: /bin/bash
+Provided cores: 1
+Rules claiming more threads will be scaled down.
+Job counts:
+	count	jobs
+	1	all
+	1	run_fastp_paired
+	2
+
+[Mon Jan 28 09:40:58 2019]
+Job 1: Running fastp on files /home/aa/pipeline_dev/Allmine/testdata/ecoA_1.fastq and /home/aa/pipeline_dev/Allmine/testdata/ecoA_2.fastq 
+
+
+[Mon Jan 28 09:41:10 2019]
+Finished job 1.
+1 of 2 steps (50%) done
+
+[Mon Jan 28 09:41:10 2019]
+localrule all:
+    input: /home/aa/pipeline_dev/Allmine/modules/trimmed/ecoA_1_trim.fastq.gz, /home/aa/pipeline_dev/Allmine/modules/trimmed/ecoA_2_trim.fastq.gz
+    jobid: 0
+
+[Mon Jan 28 09:41:10 2019]
+Finished job 0.
+2 of 2 steps (100%) done
+Complete log: /home/aa/pipeline_dev/Allmine/modules/.snakemake/log/2019-01-28T094058.844762.snakemake.log
diff --git a/modules/.snakemake/log/2019-01-28T094620.990952.snakemake.log b/modules/.snakemake/log/2019-01-28T094620.990952.snakemake.log
@@ -0,0 +1,27 @@
+Building DAG of jobs...
+Using shell: /bin/bash
+Provided cores: 1
+Rules claiming more threads will be scaled down.
+Job counts:
+	count	jobs
+	1	all
+	1	run_fastp_paired
+	2
+
+[Mon Jan 28 09:46:21 2019]
+Job 1: Running fastp on files /home/aa/pipeline_dev/Allmine/testdata/ecoA_1.fastq and /home/aa/pipeline_dev/Allmine/testdata/ecoA_2.fastq 
+
+
+[Mon Jan 28 09:46:32 2019]
+Finished job 1.
+1 of 2 steps (50%) done
+
+[Mon Jan 28 09:46:32 2019]
+localrule all:
+    input: /home/aa/pipeline_dev/Allmine/modules/trimmed/ecoA_1_trim.fastq.gz, /home/aa/pipeline_dev/Allmine/modules/trimmed/ecoA_2_trim.fastq.gz
+    jobid: 0
+
+[Mon Jan 28 09:46:32 2019]
+Finished job 0.
+2 of 2 steps (100%) done
+Complete log: /home/aa/pipeline_dev/Allmine/modules/.snakemake/log/2019-01-28T094620.990952.snakemake.log