The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

This release moves from an in-house snapshot of ichorCNA to the upstream nf-core (which required some fixes in ichorCNA and the bioconda package as well). It also moves away from the fragile "PoN files are gathered from a directory" to a more robust "normals are defined in the samplesheet". Notice that this version introduces significant breaking changes from the previous ones, which will require changes in workflow parameters. Make sure to read the section "Breaking changes" carefully before upgrading.

This release is named after Ashikaga Takauji (足利尊氏; 1305-1358), the founder of the Ashikaga shogunate during the Japanese Middle Ages, whose rise to power marked the beginning of the Muromachi period (1336-1576; "Muromachi" was the area of Kyoto where the Ashikaga took residence).

• A new mandatory column has been added in the samplesheet, status, which can be either normal or tumor (@lbeltrame, issue #13)
• Option --pon_path has been removed. Instead, add your normal samples to the samplesheet (same rules as case samples) with the normal status
• Due to a bug in ichorCNA with security implications, the syntax of all options regarding ichorCNA chromosome handling (but not the readcounter parameters) has changed:
  • Specify chromosomes with identifier only (without chr)
  • Valid values are individual chromosomes, separated by comma (e.g. 1 or 1,2), ranges using : (1:22) or a combination of the above (1:22, X). If you set ichorcna_genomestyle, the right prefix will be appended for you when running the analysis
  • ichorcna_plotylim now takes a min and max value separated by comma (e.g. -2,4)
  • All the ichorCNA options that require TRUE or FALSE now take a boolean true or false
  • Raw R in any ichorCNA option (e.g. c(1,2)) is no longer supported and will raise an error.

• Support the latest version of ichorCNA (@lbeltrame and @SaraPotente, PR #57)
• Fix generating panel of normals without sufficient reads on chromosome X (GavinHaLab/ichorCNA#26; bioconda/bioconda-recipes#61045; nf-core/modules#9531)
• Update the ichorCNA modules to the latest upstream nf-core versions (@lbeltrame, PR #57)
• PoN support in the samplesheet (@lbeltrame, #13, PR #57)

• Don't raise an error if in CIN quantification there is only one sample (#59, @lbeltrame)

This release is a hotfix for a regression in size selection that somehow slipped under the radar. Mori Ranmaru (森蘭丸, 1565-1582) was a retainer of warlord Oda Nobunaga during the Sengoku period, kown for his loyalty to his master.

• Pass the right number of arguments to samtools view (@lbeltrame, c9e8b012e60c1ed9d9e0a4b88431fc51478b6d22)

This release brings a few bug fixes and a large internal rerorganization to make the pipeline more robust. There are also a few new features, like better alignment parameters in BWA for cfDNA, support for read groups in BAM, and initial work towards using upstream nf-core modules.

This release is named after Uesugi Kenshin (上杉謙信, 1530-1578), also known as 越後の龍 (the dragon of Echigo), a powerful warrior ruling over the province of Echigo during the Sengoku period of feudal Japan. Kenshin and Takeda Shingen were notoriously rivals, and they allegedly fought against each other in personal combat during the fourth battle of Kawanakajima (1561).

• Support read groups (#54), @lbeltrame)
• Use optimized parameters for BWA alignment when dealing with cfDNA (#36, @lbeltrame) - Thanks to @SPPearce for the insight!
• Rename broad and focal in GISTIC output to long and short respectively to reduce the confusion with broad and focal lesions as defined by GISTIC itself (c3d17b840f90aaddeea123c46fe3e2ebbaebb3fc, @lbeltrame)

• Make pipeline parameters conditional (#23, @lbeltrame)
• Clamp ploidy aware log2ratios to -0.5 as lower bound to prevent nonsense results (e.g., -7) (6c02573f6ff9fee472760b3d79671547160d5665, @lbeltrame)

• Remove usage of params as much as possible (#21, @lbeltrame)
• Use the upstream nf-core WisecondorX module and workflow(PR #51, @lbeltrame)
• Switch liquid biopsy to the common ichorCNA workflow (PR #55, @lbeltrame)

This release is a hotfix to ensure that ichorCNA panel of normals (PoN) built during the analysis (as opposed to using a pre-made one) will actually be used (before that the would get copied, but not included in the ichorCNA commands).

• Honor the PoN used, either as CLI argument or built during analysis(830f9e56597a4f351915440a838a051f454dd00c, @lbeltrame)

This release fixes a critical bug in the logR correction for GISTIC in ichorCNA, which caused wrong logR values to be generated. In addition, there are other fixes in ichorCNA (in particular now PoNs in data without chromosome X can be generated) and a small new feature (absolute integer CN in ASCAT.sc). Nitta Yoshisada (新田義貞, 1301-1338) was a samurai lord during the Nanboku-cho period in Japan, also briefly involved in the wars following the so-called "Kenmu Restoration".

• Add integer absolute copy numbers to ASCAT.sc (#38, @SaraPotente)

• Fix GISTIC logR correction in ichorCNA (@lbeltrame, 002273536314d96f8446ee0e9cd84836af7ccf45)
• Make sure the ichorCNA PoN generation works even in absence of data on chrX ( 5e292cef413676448f503f97660c395ee9ba0d99, @lbeltrame)

This release fixes a bug in the workflow caused by the new genomic plotting feature in the ichorCNA workflow.

Shibata Katsuie (柴田勝家; 1522-1583), also known with the name of Gonroku (権六) was a retainer of the Nobunaga clan, serving under Oda Nobuhide and Oda Nobunaga during the "Warring States" period in Japan.

• Fix undefined output variable (9418166871a6504ea25470af5e8ef2393f216664, @SaraPotente)

This release fixes a bug in the new ichorCNA plotting introduced in version 1.2.0: plotting would not work due to a missing dependency in the container. A new container image has been made to correct this problem.

Maeda Toshiie (前田利家; 1538-1599), also known as "Yari no Mataza" (槍の又左) was a leading general under Oda Nobunaga during the "Warring States" period in Japan.

• Add missing svglite dependency to the container (3a0f0760617bc1749614305b2883c4c19c114d00)

This release adds support for ichorCNA in the solid biopsy workflow (see PR #42 for caveats) and new ploidy-aware plots for ichorCNA (off by default), which can be enabled by specifying the option --ichorcna_ploidy_aware_plot.

This release is named after Ohori Tsuruhime (大祝鶴姫; 1526–1543), an "onna-musha" (female warrior) who lived and fought during the "Warring States" period in Japan. A suit of armor allegedly belonging to Tsuruhime is kept in the treasure hall of Oyamazumi Shrine, on the island of Omishima.

• New plots for ichorCNA output (PR #44, @SaraPotente)
• Allow ichorCNA also in the solid biopsy workflow (PR #42, @lbeltrame)

• Move ichorCNA to a separate subworkflow

• Integration of HRDCNA module for HRDCNA score detection in solid biopsy subworkflow (PR #35, @SaraPotente)

Takeda Shingen (1521-1573) was a warlord who ruled the province of Kai during the "Warring States" period.

• Fix genomic plot concatenations when running under Docker (#32)
• Allow running WisecondorX with size selection (8824631a699a33fa66fbe9c6b0021e021a64272f)

• Don't try to be smart with HMMcopy's ReadCounter (1bbae5755acda8574b508ab93481fb5d0268cfc5)

• Add usage docs (PR #31, @SaraPotente) (#14)

• Rename test_ascat profile to test

• Fix generating WisecondorX plots (@lbeltrame) (#28)

• Initial work towards implementation of a test profile (@SaraPotente) (#6)

• Fix downloading genomes from iGenomes (#19)
• Fix a pipeline hang when a panel of normals was built at the same time as an ichorCNA run (#20)

• Fix CIN signature output file detection.

• Bump container version for gistic-cli to fix an off-by-one error in upstream gistic-cli.

Initial release of dincalcilab/samurai, created with the nf-core template.