Pipeline release version 0.18.1
Release notes
In addition to release 0.18., a little dependency was added the to variantCallingReport for reference genome provided runs that could have caused an error.
Changes from previous stable release:
69: Adjusted the remaining input and report files to work with and without provided reference genome
68: Adjusted the final report so that it runs also without provided reference genome
67: Input files changed for final report so that pipeline dependencies work without provided reference genome
66: Exception handling if the first sample does not have reads aligned to reference genome. Now the sample with the most alignemtns is used for visualisation (instead of the first one)
65: Missing variables added for variatn calling report
64: Fixed dependencies from the report
63: Server resource allocation for the Insilico standalo report added to the server default file
62: Pairwise comparisons added to the report
61: More chapter explanations added to the QC-R-Module
60: Minimum and Maximum fragment lengths added to the basic stats report part
59: Location information added for the most covered alignment loci
58: Location names added for the most covered alignment loci
57: Small additions to the alignments-R-module (language, explanations, etc)
56: Small additions to the Cluster and Reference-R-module (language, explanations, etc)
55: Small additions to the QC-R-module (language, explanations, etc)
54: Default paths adjusted
53: Function "getConfigField" reports now only field names a row starts with
52: Added the --cluster-cancel option to the start script
51: Changed the fasta-import function in the in-silico prediction, as it might generate errors for larger genomes
50: Prepared a stand-alone In-silico report script
49: Added the In-Silico section to the final report
48: Alignment stats are determined for the size selected in-silico prediction alignments
47: Alignment stats are determined for the full in-silico prediction alignments
46: Reads are now aligned agains the size selected in-silico prediction loci
45: Reads are now aligned agains the full in-silico prediction loci
44: More details on the welcoming screen
43: In situ predicted locations for ddRad digestion are now prepared and written to References/
42: Table design in Markdown adjusted
41: Cosmetics for finalReport, status messages printed into the final report were removed.
40: Plenty of scatterplots added to related metrics to sequencing depth
39: More exportable tables added
38: Harmonised the plot colours in the final report
37: Added more descriptions to the final report
36: Deduplication vs Coverage plot added
35: QC tables display now the full dataset, without any threshold
34: QC tables can now be exported
33: Server config information added to the reports
32: QC plots now show ommit the missing R2 output (and do not duplicate R1 to pretend it to be R2)
31: Expection added in finalReport in case FastQC/MultiQC report different binnings in their reports for R1 and R2
30: Internal improvement: Duplicated Chunk names in report-knitr files are allowed
29: Paths in the configuration file can now be relative
28: Special case for flanking site determination caught (in case alignment starts at base 0, bed could have been negativ)
27: FinalReport polished and more statistics added
26: Chapter "Individual analysis" added to the finalReport
25: FinalReport: The ACGT-plot was improved in readability
24: FinalReport: Total sequences stats report now table with samples with less than 100k reads
23: Bugfix, flanking sequence extraction ignored the first alignment
22: flanking bed files are now tab-delimted, as reqired by bedtools
21: Header lines removed from Stringtie output to ensure strict gtf compatability
20: Variant calling missingnes in percentages are now displayed on a fixed 0-100 scale
19: Added the Gini coefficient to represent the concentration of reads against the different alignment loci
18: Added the correlation plot for th loci aligned to reference genome
17: Critical bugfix in 'Mockrefloci_vs_samplealignments' that crashed the pipeline byt wrong output-filename
16: QC diverging samples are now printed for upper and lower throeshols in finalReport
15: Missing percentages are now always displayed on a scale between 0 and 100%
14: summaryTable cluster to reference genome added to the final report
13: Caught the special case, if the "genome" is also part of the filename of "genome" that produced an error
12: Dependency of preliminary mock vcf added to the report to avoid errors
11: QC module cleaned up (needs still a little)
10: Added a fasta-index dependency to avoid crashes in case fasta index was not created before stats are calculated
9: Fixed hard-coded link to docker container in Module 3 (r-gbs)
8: Special case caught, in case a reference aligned bam is empty
7: Flanking sites from individual alignments are now extracted
6: Input bug in the preparesamplesheet.R script fixed (tab-delimited input enforced)
5: Removed for the time-being the R2 reads from raw-read FastQC, due to some bug in function.
4: Created functions to handle individual fastq files in FastQC report
3: Variant Calling report added
2: Added a server-small config to downscale the server requirements for smaller projects
1: Define a TMPDIR for the create vertical ref rules, as it seems to crash for large datasets when the system default tmp folder is small
What's Changed
Full Changelog: 0.16.1...0.18.1
