diff --git a/packages/2022_Kennett_Belize/2022_Kennett_Belize.config b/packages/2022_Kennett_Belize/2022_Kennett_Belize.config new file mode 100644 index 0000000..b70f0c9 --- /dev/null +++ b/packages/2022_Kennett_Belize/2022_Kennett_Belize.config @@ -0,0 +1,41 @@ +// Keep track of config versions +minotaur_release='0.4.0dev' // The release tag of the poseidon-eager repository used for processing and config file retrieval +config_template_version='0.3.0dev' +package_config_version='0.3.0dev' +minotaur_config_base="https://raw.githubusercontent.com/poseidon-framework/poseidon-eager/${minotaur_release}/conf" + +// This configuration file is designed to be a used with the nf-core/eager pipeline. +// Instead of having to specify all other configurations for the Minotaur pipeline +// on runtime, they are all contained in this file and loaded automatically upon +// specifying this config file during runtime. Additionally, any parameters that +// need to be altered from the defaults can be specified here. +// +// The intention is to make it easy for users to understand and reproduce the output +// from processing with the Minotaur workflow processing from the contents of a +// single file. + +// Load configuration profiles. They are loaded from the minotaur_config_base URL, main branch. +includeConfig "${minotaur_config_base}/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA +includeConfig "${minotaur_config_base}/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing. + +// The following config file specifies BED files for on-target endogenous DNA calculation and mean coverage as well as pseudohaploid genotyping. +// TODO: Select the appropriate config for the CaptureType of the package. +includeConfig "${minotaur_config_base}/CaptureType_profiles/1240K.config" + +params { + // Keep track of config file versions used when processing + config_profile_description = "${config_profile_description}\n - config_template_version: ${config_template_version}\n - package_config_version: ${package_config_version}" + config_profile_contact = "Thiseas C. Lamnidis (@TCLamnidis)" + + /* + TODO: If you need to change any of the default processing parameters for this package + you can specify these parameters below. + Any parameters not specified in any of the config files default to their nf-core/eager default values. + + For information on all available parameters and their default values see: + https://nf-co.re/eager/2.5.1/parameters + + You can see the latest default values for parameters within poseidon-eager at: + https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config + */ +} diff --git a/packages/2022_Kennett_Belize/2022_Kennett_Belize.ssf b/packages/2022_Kennett_Belize/2022_Kennett_Belize.ssf new file mode 100644 index 0000000..6f4dd76 --- /dev/null +++ b/packages/2022_Kennett_Belize/2022_Kennett_Belize.ssf @@ -0,0 +1,42 @@ +poseidon_IDs udg library_built notes sample_accession study_accession run_accession sample_alias secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_ftp fastq_aspera fastq_bytes fastq_md5 read_count submitted_ftp +I24541 half ds n/a SAMEA11646645 PRJEB49391 ERR7735759 I24541 ERS9293353 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24541.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/009/ERR7735759/ERR7735759.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/009/ERR7735759/ERR7735759.fastq.gz 1855984 b94d512e41912a947d15b4b24e3483cc 84417 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735759/I24541.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735759/I24541.1240k.bam.bai +I19169 half ss n/a SAMEA11646647 PRJEB49391 ERR7735761 I19169 ERS9293355 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19169.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/001/ERR7735761/ERR7735761.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/001/ERR7735761/ERR7735761.fastq.gz 92206050 6e7dd354c9c77956e490af0fb1f554e3 4025686 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735761/I19169.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735761/I19169.1240k.bam.bai +I20428 half ss n/a SAMEA11646649 PRJEB49391 ERR7735763 I20428 ERS9293357 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I20428.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/003/ERR7735763/ERR7735763.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/003/ERR7735763/ERR7735763.fastq.gz 57236928 1ca1027cb3fcba7418ff08472858cc2d 2354550 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735763/I20428.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735763/I20428.1240k.bam.bai +I24540 half ds n/a SAMEA11646650 PRJEB49391 ERR7735764 I24540 ERS9293358 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24540.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/004/ERR7735764/ERR7735764.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/004/ERR7735764/ERR7735764.fastq.gz 95187043 da8dec8b26e3c861c413a14e53f9a1b1 3717844 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735764/I24540.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735764/I24540.1240k.bam.bai +I3442 half ds n/a SAMEA11646653 PRJEB49391 ERR7735767 I3442 ERS9293361 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I3442.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/007/ERR7735767/ERR7735767.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/007/ERR7735767/ERR7735767.fastq.gz 498864434 8566ddacdd71bb872935254bf370d297 15675937 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735767/I3442.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735767/I3442.1240k.bam.bai +I19942 half ss n/a SAMEA11646654 PRJEB49391 ERR7735768 I19942 ERS9293362 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19942.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/008/ERR7735768/ERR7735768.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/008/ERR7735768/ERR7735768.fastq.gz 93890963 0925368e9095940e3af86fbcbf5cd94e 4131260 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735768/I19942.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735768/I19942.1240k.bam.bai +I19944 half ss n/a SAMEA11646656 PRJEB49391 ERR7735770 I19944 ERS9293364 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19944.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/000/ERR7735770/ERR7735770.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/000/ERR7735770/ERR7735770.fastq.gz 108012101 499cc8ea527239722020ba144ad2b90c 4740168 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735770/I19944.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735770/I19944.1240k.bam.bai +I19950 half ss n/a SAMEA11646659 PRJEB49391 ERR7735773 I19950 ERS9293367 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19950.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/003/ERR7735773/ERR7735773.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/003/ERR7735773/ERR7735773.fastq.gz 191943173 42e9cf1d1b386b77ef3ca8b0ceb6d6bf 6765002 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735773/I19950.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735773/I19950.1240k.bam.bai +I3442 half ds n/a SAMEA11646653 PRJEB49391 ERR7735779 I3442 ERS9293361 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I3442_all.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/009/ERR7735779/ERR7735779.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/009/ERR7735779/ERR7735779.fastq.gz 776592779 2bf8e4a23db81bae07c535c9e9e5cadc 24639708 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735779/I3442_all.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735779/I3442_all.1240k.bam.bai +I19169 half ss n/a SAMEA11646647 PRJEB49391 ERR7735782 I19169 ERS9293355 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19169.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/002/ERR7735782/ERR7735782.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/002/ERR7735782/ERR7735782.fastq.gz 72105 5bf37f58045d5831f779230731f0ebc4 3514 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735782/I19169.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735782/I19169.mt.bam.bai +I20428 half ss n/a SAMEA11646649 PRJEB49391 ERR7735784 I20428 ERS9293357 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I20428.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/004/ERR7735784/ERR7735784.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/004/ERR7735784/ERR7735784.fastq.gz 33445 a2f1105261d91e17ac4e976caa12e804 1393 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735784/I20428.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735784/I20428.mt.bam.bai +I5454 half ds n/a SAMEA11646652 PRJEB49391 ERR7735787 I5454 ERS9293360 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I5454.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/007/ERR7735787/ERR7735787.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/007/ERR7735787/ERR7735787.fastq.gz 521333 7b8ec25f512e7615989c98642c507a0c 24233 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735787/I5454.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735787/I5454.mt.bam.bai +I19942 half ss n/a SAMEA11646654 PRJEB49391 ERR7735789 I19942 ERS9293362 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19942.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/009/ERR7735789/ERR7735789.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/009/ERR7735789/ERR7735789.fastq.gz 201223 4fa2d37ae8078c52a53a62483cd7a5e2 11003 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735789/I19942.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735789/I19942.mt.bam.bai +I19167 half ss n/a SAMEA11646655 PRJEB49391 ERR7735790 I19167 ERS9293363 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19167.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/000/ERR7735790/ERR7735790.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/000/ERR7735790/ERR7735790.fastq.gz 28234 418e5ee553ed13d1d3c121801b1a8679 1180 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735790/I19167.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735790/I19167.mt.bam.bai +I19944 half ss n/a SAMEA11646656 PRJEB49391 ERR7735791 I19944 ERS9293364 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19944.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/001/ERR7735791/ERR7735791.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/001/ERR7735791/ERR7735791.fastq.gz 42701 a477939efc88ac3b22e704b4bbe849b6 1943 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735791/I19944.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735791/I19944.mt.bam.bai +I24542 half ds n/a SAMEA11646658 PRJEB49391 ERR7735793 I24542 ERS9293366 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24542.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/003/ERR7735793/ERR7735793.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/003/ERR7735793/ERR7735793.fastq.gz 289822 0731e7a608ce9fd572670b198a68b677 16004 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735793/I24542.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735793/I24542.mt.bam.bai +I5455 half ds n/a SAMEA11646662 PRJEB49391 ERR7735797 I5455 ERS9293370 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I5455.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/007/ERR7735797/ERR7735797.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/007/ERR7735797/ERR7735797.fastq.gz 784884 f1c74a968f9b13207d2cce0a2762811b 35846 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735797/I5455.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735797/I5455.mt.bam.bai +I8041 half ds n/a SAMEA11646663 PRJEB49391 ERR7735777 I8041 ERS9293371 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I8041.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/007/ERR7735777/ERR7735777.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/007/ERR7735777/ERR7735777.fastq.gz 18380223 2b8d1b8cc01480ade292e25db801cf0b 603701 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735777/I8041.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735777/I8041.1240k.bam.bai +I24540 half ds n/a SAMEA11646650 PRJEB49391 ERR7735785 I24540 ERS9293358 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24540.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/005/ERR7735785/ERR7735785.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/005/ERR7735785/ERR7735785.fastq.gz 148274 ce23b18682cf1ec9e69832dd9e40c016 7854 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735785/I24540.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735785/I24540.mt.bam.bai +I13267 half ds n/a SAMEA11646651 PRJEB49391 ERR7735786 I13267 ERS9293359 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I13267.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/006/ERR7735786/ERR7735786.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/006/ERR7735786/ERR7735786.fastq.gz 1272330 ab15325f3cf4ab7b56617a7d2d262fbc 67580 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735786/I13267.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735786/I13267.mt.bam.bai +I7544 half ds n/a SAMEA11646657 PRJEB49391 ERR7735792 I7544 ERS9293365 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I7544.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/002/ERR7735792/ERR7735792.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/002/ERR7735792/ERR7735792.fastq.gz 648567 d14f517afbc4afbb683b2ff6970b8978 29401 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735792/I7544.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735792/I7544.mt.bam.bai +I6236 half ds n/a SAMEA11646661 PRJEB49391 ERR7735796 I6236 ERS9293369 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I6236.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/006/ERR7735796/ERR7735796.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/006/ERR7735796/ERR7735796.fastq.gz 795676 e002bcc601b5c9e688c8f9fcec2e3113 33015 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735796/I6236.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735796/I6236.mt.bam.bai +I8041 half ds n/a SAMEA11646663 PRJEB49391 ERR7735798 I8041 ERS9293371 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I8041.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/008/ERR7735798/ERR7735798.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/008/ERR7735798/ERR7735798.fastq.gz 162249 d7d9439ea412afe12a06c12931c1c2ec 7073 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735798/I8041.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735798/I8041.mt.bam.bai +I19170 half ss n/a SAMEA11646648 PRJEB49391 ERR7735762 I19170 ERS9293356 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19170.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/002/ERR7735762/ERR7735762.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/002/ERR7735762/ERR7735762.fastq.gz 102399157 7073896ad40b7e7c4a447b0a55a3c817 4546278 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735762/I19170.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735762/I19170.1240k.bam.bai +I19167 half ss n/a SAMEA11646655 PRJEB49391 ERR7735769 I19167 ERS9293363 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19167.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/009/ERR7735769/ERR7735769.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/009/ERR7735769/ERR7735769.fastq.gz 24293929 30c12091d3f8fe7f78898b41d5018607 1033145 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735769/I19167.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735769/I19167.1240k.bam.bai +I13268 half ds n/a SAMEA11646646 PRJEB49391 ERR7735781 I13268 ERS9293354 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I13268.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/001/ERR7735781/ERR7735781.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/001/ERR7735781/ERR7735781.fastq.gz 115094 f87566e3c39293ac6026d6a255389f86 5869 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735781/I13268.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735781/I13268.mt.bam.bai +I19170 half ss n/a SAMEA11646648 PRJEB49391 ERR7735783 I19170 ERS9293356 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19170.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/003/ERR7735783/ERR7735783.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/003/ERR7735783/ERR7735783.fastq.gz 77913 3b04ff0592c6f3816f96bc2c0b01b3e3 3879 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735783/I19170.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735783/I19170.mt.bam.bai +I3422 half ds n/a SAMEA11646653 PRJEB49391 ERR7735788 I3442 ERS9293361 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I3442.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/008/ERR7735788/ERR7735788.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/008/ERR7735788/ERR7735788.fastq.gz 501741 7e0e87abecf9b5efa09dbd55bd3156a6 23147 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735788/I3442.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735788/I3442.mt.bam.bai +I5454 half ds n/a SAMEA11646652 PRJEB49391 ERR7735766 I5454 ERS9293360 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I5454.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/006/ERR7735766/ERR7735766.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/006/ERR7735766/ERR7735766.fastq.gz 163253161 ea871baba48abc0f16d4511ae22d15b3 4944463 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735766/I5454.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735766/I5454.1240k.bam.bai +I7544 half ds n/a SAMEA11646657 PRJEB49391 ERR7735771 I7544 ERS9293365 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I7544.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/001/ERR7735771/ERR7735771.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/001/ERR7735771/ERR7735771.fastq.gz 367744844 245ea1075af45d30d3e5f6b5848aaf49 11753217 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735771/I7544.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735771/I7544.1240k.bam.bai +I6235 half ds n/a SAMEA11646660 PRJEB49391 ERR7735774 I6235 ERS9293368 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I6235.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/004/ERR7735774/ERR7735774.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/004/ERR7735774/ERR7735774.fastq.gz 287480585 3146050b10350356236efd02aabf085f 8818072 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735774/I6235.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735774/I6235.1240k.bam.bai +I7543 half ss n/a SAMEA11646664 PRJEB49391 ERR7735778 I7543 ERS9293372 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I7543.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/008/ERR7735778/ERR7735778.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/008/ERR7735778/ERR7735778.fastq.gz 61592426 99fc43f8725e3beb25a4ae993171a502 2409685 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735778/I7543.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735778/I7543.1240k.bam.bai +I19950 half ss n/a SAMEA11646659 PRJEB49391 ERR7735794 I19950 ERS9293367 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19950.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/004/ERR7735794/ERR7735794.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/004/ERR7735794/ERR7735794.fastq.gz 233670 6b569cbab201211164d110dfdd077ff4 11862 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735794/I19950.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735794/I19950.mt.bam.bai +I6235 half ds n/a SAMEA11646660 PRJEB49391 ERR7735795 I6235 ERS9293368 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I6235.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/005/ERR7735795/ERR7735795.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/005/ERR7735795/ERR7735795.fastq.gz 771971 2fdc7c35481530845dfa1934578cac47 34809 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735795/I6235.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735795/I6235.mt.bam.bai +I7543 half ds n/a SAMEA11646664 PRJEB49391 ERR7735799 I7543 ERS9293372 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I7543.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/009/ERR7735799/ERR7735799.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/009/ERR7735799/ERR7735799.fastq.gz 93561 27738b9ec0e02f8fcf035e2ff27a6302 4295 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735799/I7543.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735799/I7543.mt.bam.bai +I13268 half ss n/a SAMEA11646646 PRJEB49391 ERR7735760 I13268 ERS9293354 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I13268.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/000/ERR7735760/ERR7735760.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/000/ERR7735760/ERR7735760.fastq.gz 153779107 a9346a5a151ac8b06b80220d3a110b06 6415547 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735760/I13268.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735760/I13268.1240k.bam.bai +I13267 half ds n/a SAMEA11646651 PRJEB49391 ERR7735765 I13267 ERS9293359 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I13267.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/005/ERR7735765/ERR7735765.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/005/ERR7735765/ERR7735765.fastq.gz 382102409 546573064bb13a22915b94886d1bc958 13317936 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735765/I13267.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735765/I13267.1240k.bam.bai +I24542 half ds n/a SAMEA11646658 PRJEB49391 ERR7735772 I24542 ERS9293366 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24542.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/002/ERR7735772/ERR7735772.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/002/ERR7735772/ERR7735772.fastq.gz 290069082 c2c1ba335d30bd3ff43cb9272d782cf3 11630634 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735772/I24542.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735772/I24542.1240k.bam.bai +I6236 half ds n/a SAMEA11646661 PRJEB49391 ERR7735775 I6236 ERS9293369 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I6236.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/005/ERR7735775/ERR7735775.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/005/ERR7735775/ERR7735775.fastq.gz 359469846 3f4edc6f41c196641e5a9be058069dab 10062021 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735775/I6236.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735775/I6236.1240k.bam.bai +I5455 half ds n/a SAMEA11646662 PRJEB49391 ERR7735776 I5455 ERS9293370 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I5455.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/006/ERR7735776/ERR7735776.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/006/ERR7735776/ERR7735776.fastq.gz 237496024 791ad7c50b0a9e04aad6295de11b7ada 7141310 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735776/I5455.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735776/I5455.1240k.bam.bai +I24541 half ds n/a SAMEA11646645 PRJEB49391 ERR7735780 I24541 ERS9293353 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24541.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/000/ERR7735780/ERR7735780.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/000/ERR7735780/ERR7735780.fastq.gz 3084 f131746da555866f47a7b72033e5567f 101 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735780/I24541.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735780/I24541.mt.bam.bai diff --git a/packages/2022_Kennett_Belize/2022_Kennett_Belize.tsv b/packages/2022_Kennett_Belize/2022_Kennett_Belize.tsv new file mode 100644 index 0000000..8b459e5 --- /dev/null +++ b/packages/2022_Kennett_Belize/2022_Kennett_Belize.tsv @@ -0,0 +1,42 @@ +Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_Treatment R1 R2 BAM R1_target_file R2_target_file +I24541 I24541_I24541.1240k 1 4 SE Homo sapiens (modern human) double half /I24541_I24541.1240k_L1_R1.fastq.gz NA NA ERR7735759.fastq.gz NA +I19169_ss I19169_ss_I19169.1240k_ss 1 4 SE Homo sapiens (modern human) single half /I19169_ss_I19169.1240k_ss_L1_R1.fastq.gz NA NA ERR7735761.fastq.gz NA +I20428_ss I20428_ss_I20428.1240k_ss 1 4 SE Homo sapiens (modern human) single half /I20428_ss_I20428.1240k_ss_L1_R1.fastq.gz NA NA ERR7735763.fastq.gz NA +I24540 I24540_I24540.1240k 1 4 SE Homo sapiens (modern human) double half /I24540_I24540.1240k_L1_R1.fastq.gz NA NA ERR7735764.fastq.gz NA +I3442 I3442_I3442.1240k 1 4 SE Homo sapiens (modern human) double half /I3442_I3442.1240k_L1_R1.fastq.gz NA NA ERR7735767.fastq.gz NA +I19942_ss I19942_ss_I19942.1240k_ss 1 4 SE Homo sapiens (modern human) single half /I19942_ss_I19942.1240k_ss_L1_R1.fastq.gz NA NA ERR7735768.fastq.gz NA +I19944_ss I19944_ss_I19944.1240k_ss 1 4 SE Homo sapiens (modern human) single half /I19944_ss_I19944.1240k_ss_L1_R1.fastq.gz NA NA ERR7735770.fastq.gz NA +I19950_ss I19950_ss_I19950.1240k_ss 1 4 SE Homo sapiens (modern human) single half /I19950_ss_I19950.1240k_ss_L1_R1.fastq.gz NA NA ERR7735773.fastq.gz NA +I3442 I3442_I3442_all.1240k 1 4 SE Homo sapiens (modern human) double half /I3442_I3442_all.1240k_L1_R1.fastq.gz NA NA ERR7735779.fastq.gz NA +I19169_ss I19169_ss_I19169.mt_ss 1 4 SE Homo sapiens (modern human) single half /I19169_ss_I19169.mt_ss_L1_R1.fastq.gz NA NA ERR7735782.fastq.gz NA +I20428_ss I20428_ss_I20428.mt_ss 1 4 SE Homo sapiens (modern human) single half /I20428_ss_I20428.mt_ss_L1_R1.fastq.gz NA NA ERR7735784.fastq.gz NA +I5454 I5454_I5454.mt 1 4 SE Homo sapiens (modern human) double half /I5454_I5454.mt_L1_R1.fastq.gz NA NA ERR7735787.fastq.gz NA +I19942_ss I19942_ss_I19942.mt_ss 1 4 SE Homo sapiens (modern human) single half /I19942_ss_I19942.mt_ss_L1_R1.fastq.gz NA NA ERR7735789.fastq.gz NA +I19167_ss I19167_ss_I19167.mt_ss 1 4 SE Homo sapiens (modern human) single half /I19167_ss_I19167.mt_ss_L1_R1.fastq.gz NA NA ERR7735790.fastq.gz NA +I19944_ss I19944_ss_I19944.mt_ss 1 4 SE Homo sapiens (modern human) single half /I19944_ss_I19944.mt_ss_L1_R1.fastq.gz NA NA ERR7735791.fastq.gz NA +I24542 I24542_I24542.mt 1 4 SE Homo sapiens (modern human) double half /I24542_I24542.mt_L1_R1.fastq.gz NA NA ERR7735793.fastq.gz NA +I5455 I5455_I5455.mt 1 4 SE Homo sapiens (modern human) double half /I5455_I5455.mt_L1_R1.fastq.gz NA NA ERR7735797.fastq.gz NA +I8041 I8041_I8041.1240k 1 4 SE Homo sapiens (modern human) double half /I8041_I8041.1240k_L1_R1.fastq.gz NA NA ERR7735777.fastq.gz NA +I24540 I24540_I24540.mt 1 4 SE Homo sapiens (modern human) double half /I24540_I24540.mt_L1_R1.fastq.gz NA NA ERR7735785.fastq.gz NA +I13267 I13267_I13267.mt 1 4 SE Homo sapiens (modern human) double half /I13267_I13267.mt_L1_R1.fastq.gz NA NA ERR7735786.fastq.gz NA +I7544 I7544_I7544.mt 1 4 SE Homo sapiens (modern human) double half /I7544_I7544.mt_L1_R1.fastq.gz NA NA ERR7735792.fastq.gz NA +I6236 I6236_I6236.mt 1 4 SE Homo sapiens (modern human) double half /I6236_I6236.mt_L1_R1.fastq.gz NA NA ERR7735796.fastq.gz NA +I8041 I8041_I8041.mt 1 4 SE Homo sapiens (modern human) double half /I8041_I8041.mt_L1_R1.fastq.gz NA NA ERR7735798.fastq.gz NA +I19170_ss I19170_ss_I19170.1240k_ss 1 4 SE Homo sapiens (modern human) single half /I19170_ss_I19170.1240k_ss_L1_R1.fastq.gz NA NA ERR7735762.fastq.gz NA +I19167_ss I19167_ss_I19167.1240k_ss 1 4 SE Homo sapiens (modern human) single half /I19167_ss_I19167.1240k_ss_L1_R1.fastq.gz NA NA ERR7735769.fastq.gz NA +I13268 I13268_I13268.mt 1 4 SE Homo sapiens (modern human) double half /I13268_I13268.mt_L1_R1.fastq.gz NA NA ERR7735781.fastq.gz NA +I19170_ss I19170_ss_I19170.mt_ss 1 4 SE Homo sapiens (modern human) single half /I19170_ss_I19170.mt_ss_L1_R1.fastq.gz NA NA ERR7735783.fastq.gz NA +I3422 I3422_I3442.mt 1 4 SE Homo sapiens (modern human) double half /I3422_I3442.mt_L1_R1.fastq.gz NA NA ERR7735788.fastq.gz NA +I5454 I5454_I5454.1240k 1 4 SE Homo sapiens (modern human) double half /I5454_I5454.1240k_L1_R1.fastq.gz NA NA ERR7735766.fastq.gz NA +I7544 I7544_I7544.1240k 1 4 SE Homo sapiens (modern human) double half /I7544_I7544.1240k_L1_R1.fastq.gz NA NA ERR7735771.fastq.gz NA +I6235 I6235_I6235.1240k 1 4 SE Homo sapiens (modern human) double half /I6235_I6235.1240k_L1_R1.fastq.gz NA NA ERR7735774.fastq.gz NA +I7543_ss I7543_ss_I7543.1240k_ss 1 4 SE Homo sapiens (modern human) single half /I7543_ss_I7543.1240k_ss_L1_R1.fastq.gz NA NA ERR7735778.fastq.gz NA +I19950_ss I19950_ss_I19950.mt_ss 1 4 SE Homo sapiens (modern human) single half /I19950_ss_I19950.mt_ss_L1_R1.fastq.gz NA NA ERR7735794.fastq.gz NA +I6235 I6235_I6235.mt 1 4 SE Homo sapiens (modern human) double half /I6235_I6235.mt_L1_R1.fastq.gz NA NA ERR7735795.fastq.gz NA +I7543 I7543_I7543.mt 1 4 SE Homo sapiens (modern human) double half /I7543_I7543.mt_L1_R1.fastq.gz NA NA ERR7735799.fastq.gz NA +I13268_ss I13268_ss_I13268.1240k_ss 1 4 SE Homo sapiens (modern human) single half /I13268_ss_I13268.1240k_ss_L1_R1.fastq.gz NA NA ERR7735760.fastq.gz NA +I13267 I13267_I13267.1240k 1 4 SE Homo sapiens (modern human) double half /I13267_I13267.1240k_L1_R1.fastq.gz NA NA ERR7735765.fastq.gz NA +I24542 I24542_I24542.1240k 1 4 SE Homo sapiens (modern human) double half /I24542_I24542.1240k_L1_R1.fastq.gz NA NA ERR7735772.fastq.gz NA +I6236 I6236_I6236.1240k 1 4 SE Homo sapiens (modern human) double half /I6236_I6236.1240k_L1_R1.fastq.gz NA NA ERR7735775.fastq.gz NA +I5455 I5455_I5455.1240k 1 4 SE Homo sapiens (modern human) double half /I5455_I5455.1240k_L1_R1.fastq.gz NA NA ERR7735776.fastq.gz NA +I24541 I24541_I24541.mt 1 4 SE Homo sapiens (modern human) double half /I24541_I24541.mt_L1_R1.fastq.gz NA NA ERR7735780.fastq.gz NA diff --git a/packages/2022_Kennett_Belize/2022_Kennett_Belize.tsv_patch.sh b/packages/2022_Kennett_Belize/2022_Kennett_Belize.tsv_patch.sh new file mode 100755 index 0000000..a73f9af --- /dev/null +++ b/packages/2022_Kennett_Belize/2022_Kennett_Belize.tsv_patch.sh @@ -0,0 +1,45 @@ +#!/usr/bin/env bash +set -uo pipefail ## Pipefail, complain on new unassigned variables. + +## Track the version of the TSV_patch template used +VERSION='0.2.1dev' + +## This script is applied to the eager input TSV file locally to edit the dummy +## path to the fastQ files added by `create_eager_input.sh` to a real local +## path provided as a positional argument. Any further local tweaks to the +## TSV before running eager should be added below that in the form of bash +## commands to aid in reproducibility. + +## usage tsv_patch.sh + +local_data_dir="$(readlink -f ${1})" +input_tsv="$(readlink -f ${2})" +output_tsv="$(dirname ${local_data_dir})/$(basename -s ".tsv" ${input_tsv}).finalised.tsv" +columns_to_keep=("Sample_Name" "Library_ID" "Lane" "Colour_Chemistry" "SeqType" "Organism" "Strandedness" "UDG_Treatment" "R1" "R2" "BAM") +source $(readlink -f ${3}) ## Path to helper function script should be provided as 3rd argument. https://github.com/poseidon-framework/poseidon-eager/blob/main/scripts/source_me.sh + +## Index non-proliferated columns and exclude them from the finalised TSV +cut_selector='' +tsv_header=($(head -n1 ${input_tsv})) +for col_name in ${columns_to_keep[@]}; do + let idx=$(get_index_of ${col_name} "${columns_to_keep[@]}")+1 ## awk uses 1-based indexing + if [[ ! ${idx} -eq -1 ]]; then + cut_selector+="${idx}," + fi +done + +## Remove added columns, and put columns in right order +cut -f ${cut_selector%,} ${input_tsv} > ${output_tsv} +sed -i -e "s||${local_data_dir}|g" ${output_tsv} + +## Any further commands to edit the file before finalisation should be added below as shown +# sed -ie 's/replace_this/with_this/g' ${output_tsv} + +## Keep track of versions +version_file="$(dirname ${input_tsv})/script_versions.txt" +## Remove versions from older run if there +grep -v -F -e "$(basename ${0})" -e "source_me.sh for final TSV" ${version_file} >${version_file}.new +## Then add new versions +echo -e "$(basename ${0}):\t${VERSION}" >> ${version_file}.new +echo -e "source_me.sh for final TSV:\t${HELPER_FUNCTION_VERSION}" >>${version_file}.new +mv ${version_file}.new ${version_file} diff --git a/packages/2022_Kennett_Belize/script_versions.txt b/packages/2022_Kennett_Belize/script_versions.txt new file mode 100644 index 0000000..7a83b10 --- /dev/null +++ b/packages/2022_Kennett_Belize/script_versions.txt @@ -0,0 +1,2 @@ +create_eager_input.sh: 0.2.1dev +source_me.sh for initial TSV: 0.2.3dev