diff --git a/packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.config b/packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.config new file mode 100644 index 0000000..b70f0c9 --- /dev/null +++ b/packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.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/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.ssf b/packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.ssf new file mode 100644 index 0000000..b4211e5 --- /dev/null +++ b/packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.ssf @@ -0,0 +1,69 @@ +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 +CBE003_TF half ds n/a SAMEA114211430 PRJEB51863 ERR11769644 CBE003.A ERS16192115 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CBE003.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/044/ERR11769644/ERR11769644.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/044/ERR11769644/ERR11769644.fastq.gz 90523690 d0bed2a85048d63848fa5e156ab2b530 2474595 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769644/CBE003.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769644/CBE003.A0101.TF1.1.bam.bai +CUB002_TF half ds n/a SAMEA114211432 PRJEB51863 ERR11769646 CUB002.A ERS16192117 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CUB002.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/046/ERR11769646/ERR11769646.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/046/ERR11769646/ERR11769646.fastq.gz 30019484 204426585b0b845a282b26c808b35288 916802 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769646/CUB002.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769646/CUB002.A0101.TF1.1.bam.bai +GA4002_TF half ds n/a SAMEA114211440 PRJEB51863 ERR11769654 GA4002.A ERS16192125 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GA4002.A0101.TF1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/054/ERR11769654/ERR11769654.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/054/ERR11769654/ERR11769654.fastq.gz 25606139 d2cfe69d16447b8df869b3ddbb7e29ce 779052 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769654/GA4002.A1.A2.TF.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769654/GA4002.A1.A2.TF.bam.bai +JBT009_TF half ds n/a SAMEA114211443 PRJEB51863 ERR11769657 JBT009.A ERS16192128 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT009.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/057/ERR11769657/ERR11769657.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/057/ERR11769657/ERR11769657.fastq.gz 343320619 43f8abc2d1eaca40a39660beeba8d939 10358242 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769657/JBT009.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769657/JBT009.A0101.TF1.1.bam.bai +JBT011_TF half ds n/a SAMEA114211445 PRJEB51863 ERR11769659 JBT011.A ERS16192130 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT011.A0101.TF1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/059/ERR11769659/ERR11769659.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/059/ERR11769659/ERR11769659.fastq.gz 42294357 dcb49f646260a44b0a8cdb932e351f85 1265264 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769659/JBT011.A1.A2.TF.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769659/JBT011.A1.A2.TF.bam.bai +JBT015_TF half ds n/a SAMEA114211449 PRJEB51863 ERR11769663 JBT015.A ERS16192134 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT015.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/063/ERR11769663/ERR11769663.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/063/ERR11769663/ERR11769663.fastq.gz 294663639 3598053a1c076ffce2bec68dc8a52533 8139902 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769663/JBT015.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769663/JBT015.A0101.TF1.1.bam.bai +JBT025_TF half ds n/a SAMEA114211456 PRJEB51863 ERR11769670 JBT025.A ERS16192141 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT025.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/070/ERR11769670/ERR11769670.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/070/ERR11769670/ERR11769670.fastq.gz 169217546 501a74c502f0bec902bf60f02f7f1f8e 4821885 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769670/JBT025.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769670/JBT025.A0101.TF1.1.bam.bai +JBT026_TF half ds n/a SAMEA114211457 PRJEB51863 ERR11769671 JBT026.A ERS16192142 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT026.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/071/ERR11769671/ERR11769671.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/071/ERR11769671/ERR11769671.fastq.gz 166247854 826d223c1c22332ae92cc0187955297d 4956814 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769671/JBT026.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769671/JBT026.A0101.TF1.1.bam.bai +CBE004_MT half ds n/a SAMEA114211431 PRJEB51863 ERR11770484 CBE004.A ERS16192116 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CBE004.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/084/ERR11770484/ERR11770484.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/084/ERR11770484/ERR11770484.fastq.gz 68859 99ad3db32a518df8a560de11e0c363e1 2855 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770484/CBE004.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770484/CBE004.A0101.MT1.1.bam.bai +CUB002_MT half ds n/a SAMEA114211432 PRJEB51863 ERR11770485 CUB002.A ERS16192117 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CUB002.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/085/ERR11770485/ERR11770485.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/085/ERR11770485/ERR11770485.fastq.gz 154383 b2ecc6ca7c7a0d6b69f52d43799a68f4 6855 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770485/CUB002.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770485/CUB002.A0101.MT1.1.bam.bai +CUB008_MT half ds n/a SAMEA114211433 PRJEB51863 ERR11770486 CUB008.A ERS16192118 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CUB008.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/086/ERR11770486/ERR11770486.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/086/ERR11770486/ERR11770486.fastq.gz 399879 71d3b75c77b0b39fc34bfb9eb3bb4817 18578 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770486/CUB008.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770486/CUB008.A0101.MT1.1.bam.bai +EPS002_MT half ds n/a SAMEA114211435 PRJEB51863 ERR11770488 EPS002.A ERS16192120 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA EPS002.A0101.MT1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/088/ERR11770488/ERR11770488.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/088/ERR11770488/ERR11770488.fastq.gz 38880 8ae4ecee387163e8b75e52241104c8db 1322 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770488/EPS002.A0101.MT1.1_2.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770488/EPS002.A0101.MT1.1_2.bam.bai +EPS004_MT half ds n/a SAMEA114211437 PRJEB51863 ERR11770490 EPS004.A ERS16192122 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA EPS004.A0101.MT1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/090/ERR11770490/ERR11770490.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/090/ERR11770490/ERR11770490.fastq.gz 123895 05f9be903452f1675b58345880f5c944 5074 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770490/EPS004.A0101.MT1.1_2.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770490/EPS004.A0101.MT1.1_2.bam.bai +EPS005_MT half ds n/a SAMEA114211438 PRJEB51863 ERR11770491 EPS005.A ERS16192123 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA EPS005.A0101.MT1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/091/ERR11770491/ERR11770491.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/091/ERR11770491/ERR11770491.fastq.gz 221462 4b742bf7f09a42e6134e64c6bc1fc5dc 9577 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770491/EPS005.A0101.MT1.1_2.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770491/EPS005.A0101.MT1.1_2.bam.bai +JBT001_MT half ds n/a SAMEA114211441 PRJEB51863 ERR11770494 JBT001.A ERS16192126 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/094/ERR11770494/ERR11770494.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/094/ERR11770494/ERR11770494.fastq.gz 652792 cb9b8f9a2380a779f162a53b0b74e361 28919 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770494/JBT001.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770494/JBT001.A0101.MT1.1.bam.bai +JBT010_MT half ds n/a SAMEA114211444 PRJEB51863 ERR11770497 JBT010.A ERS16192129 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT010.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/097/ERR11770497/ERR11770497.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/097/ERR11770497/ERR11770497.fastq.gz 450343 48dc6f6d51620c9ee111cf4cdefa0aa1 20689 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770497/JBT010.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770497/JBT010.A0101.MT1.1.bam.bai +JBT012_MT half ds n/a SAMEA114211446 PRJEB51863 ERR11770499 JBT012.A ERS16192131 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT012.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/099/ERR11770499/ERR11770499.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/099/ERR11770499/ERR11770499.fastq.gz 577073 dad5d8efcd5bc94011d31b17a3aa17d5 26433 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770499/JBT012.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770499/JBT012.A0101.MT1.1.bam.bai +JBT015_MT half ds n/a SAMEA114211449 PRJEB51863 ERR11770502 JBT015.A ERS16192134 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT015.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/002/ERR11770502/ERR11770502.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/002/ERR11770502/ERR11770502.fastq.gz 687579 03c2d47e3a365f89281c34025208f829 31391 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770502/JBT015.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770502/JBT015.A0101.MT1.1.bam.bai +JBT020_MT half ds n/a SAMEA114211452 PRJEB51863 ERR11770505 JBT020.A ERS16192137 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT020.A0101.MT1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/005/ERR11770505/ERR11770505.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/005/ERR11770505/ERR11770505.fastq.gz 194756 ed6849ef2c3291b160d7e359ec350e5c 8775 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770505/JBT020.A0101.MT1.1_2.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770505/JBT020.A0101.MT1.1_2.bam.bai +JBT023_MT half ds n/a SAMEA114211455 PRJEB51863 ERR11770508 JBT023.A ERS16192140 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT023.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/008/ERR11770508/ERR11770508.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/008/ERR11770508/ERR11770508.fastq.gz 531398 2286196b46daed6776ee802d4cbd6a60 23918 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770508/JBT023.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770508/JBT023.A0101.MT1.1.bam.bai +JBT025_MT half ds n/a SAMEA114211456 PRJEB51863 ERR11770509 JBT025.A ERS16192141 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT025.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/009/ERR11770509/ERR11770509.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/009/ERR11770509/ERR11770509.fastq.gz 490795 4d71569c81d0ee41428de55dc9dab7f4 22294 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770509/JBT025.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770509/JBT025.A0101.MT1.1.bam.bai +SAM014_MT half ds n/a SAMEA114211460 PRJEB51863 ERR11770513 SAM014.A ERS16192145 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA SAM014.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/013/ERR11770513/ERR11770513.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/013/ERR11770513/ERR11770513.fastq.gz 614175 09e49617dbb690e1610625bafbb8fc64 32138 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770513/SAM014.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770513/SAM014.A0101.MT1.1.bam.bai +TDA002_MT minus ds n/a SAMEA114211461 PRJEB51863 ERR11770514 TDA002.A ERS16192146 2023-07-30 2023-07-30 Illumina HiSeq 4000 PAIRED METAGENOMIC ILLUMINA TDA002.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/014/ERR11770514/ERR11770514.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/014/ERR11770514/ERR11770514.fastq.gz 332042 e48bbc8d82e39312fe3a0c31b552f544 17116 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770514/TDA002.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770514/TDA002.A0101.MT1.1.bam.bai +CAP007_TF half ds n/a SAMEA114211429 PRJEB51863 ERR11769643 CAP007.A ERS16192114 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAP007.A0101.TF1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/043/ERR11769643/ERR11769643.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/043/ERR11769643/ERR11769643.fastq.gz 71637838 d0f44ca444c2eb2fed8a9faa0cb5fc53 2075045 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769643/CAP007.A1.A2.TF.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769643/CAP007.A1.A2.TF.bam.bai +EPS001_TF half ds n/a SAMEA114211434 PRJEB51863 ERR11769648 EPS001.A ERS16192119 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA EPS001.A0102.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/048/ERR11769648/ERR11769648.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/048/ERR11769648/ERR11769648.fastq.gz 244535053 c93b076395089199789f8419a679231a 6623002 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769648/EPS001.A0102.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769648/EPS001.A0102.TF1.1.bam.bai +EPS005_TF half ds n/a SAMEA114211438 PRJEB51863 ERR11769652 EPS005.A ERS16192123 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA EPS005.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/052/ERR11769652/ERR11769652.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/052/ERR11769652/ERR11769652.fastq.gz 50771393 72e107df711bc2225dfa93ef62ab7005 1400750 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769652/EPS005.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769652/EPS005.A0101.TF1.1.bam.bai +EPS011_TF half ds n/a SAMEA114211439 PRJEB51863 ERR11769653 EPS011.A ERS16192124 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA EPS011.A0101.TF1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/053/ERR11769653/ERR11769653.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/053/ERR11769653/ERR11769653.fastq.gz 47304747 6e1c7305b114e81acf8c2a1365e6720c 1449018 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769653/EPS011.A1.A2.TF.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769653/EPS011.A1.A2.TF.bam.bai +JBT001_TF half ds n/a SAMEA114211441 PRJEB51863 ERR11769655 JBT001.A ERS16192126 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT001.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/055/ERR11769655/ERR11769655.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/055/ERR11769655/ERR11769655.fastq.gz 53112674 0cfcdef10de4b5992a1b68c8c66ca05e 1490340 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769655/JBT001.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769655/JBT001.A0101.TF1.1.bam.bai +JBT002_TF half ds n/a SAMEA114211442 PRJEB51863 ERR11769656 JBT002.A ERS16192127 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT002.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/056/ERR11769656/ERR11769656.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/056/ERR11769656/ERR11769656.fastq.gz 53112733 770bcdebdc3beb268ddea74c6dfa1c42 1490340 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769656/JBT002.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769656/JBT002.A0101.TF1.1.bam.bai +JBT010_TF half ds n/a SAMEA114211444 PRJEB51863 ERR11769658 JBT010.A ERS16192129 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT010.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/058/ERR11769658/ERR11769658.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/058/ERR11769658/ERR11769658.fastq.gz 110844075 3a6c5221f108b5d2a49d2c91813556ae 3144140 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769658/JBT010.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769658/JBT010.A0101.TF1.1.bam.bai +JBT013_TF half ds n/a SAMEA114211447 PRJEB51863 ERR11769661 JBT013.A ERS16192132 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT013.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/061/ERR11769661/ERR11769661.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/061/ERR11769661/ERR11769661.fastq.gz 166241176 9773f62852612403d8ff1b262b66daab 4654952 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769661/JBT013.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769661/JBT013.A0101.TF1.1.bam.bai +JBT014_TF half ds n/a SAMEA114211448 PRJEB51863 ERR11769662 JBT014.A ERS16192133 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT014.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/062/ERR11769662/ERR11769662.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/062/ERR11769662/ERR11769662.fastq.gz 52330382 239c54275f7c3dd2b05e7e87e5fc9ac6 1376360 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769662/JBT014.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769662/JBT014.A0101.TF1.1.bam.bai +JBT019_TF half ds n/a SAMEA114211451 PRJEB51863 ERR11769665 JBT019.A ERS16192136 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT019.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/065/ERR11769665/ERR11769665.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/065/ERR11769665/ERR11769665.fastq.gz 88979498 7ca3009658c83bdc38113c486df45def 2344676 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769665/JBT019.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769665/JBT019.A0101.TF1.1.bam.bai +JBT021_TF half ds n/a SAMEA114211453 PRJEB51863 ERR11769667 JBT021.A ERS16192138 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT021.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/067/ERR11769667/ERR11769667.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/067/ERR11769667/ERR11769667.fastq.gz 138704995 c0015a754c2ab9374fe670bf6b5e3e41 3956475 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769667/JBT021.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769667/JBT021.A0101.TF1.1.bam.bai +JBT023_TF half ds n/a SAMEA114211455 PRJEB51863 ERR11769669 JBT023.A ERS16192140 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT023.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/069/ERR11769669/ERR11769669.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/069/ERR11769669/ERR11769669.fastq.gz 180222342 3936fdf75d5f79bb38e2acb601d90c9a 4945140 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769669/JBT023.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769669/JBT023.A0101.TF1.1.bam.bai +PAI001_TF half ds n/a SAMEA114211458 PRJEB51863 ERR11769672 PAI001.A ERS16192143 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PAI001.A0101.TF1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/072/ERR11769672/ERR11769672.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/072/ERR11769672/ERR11769672.fastq.gz 68276654 5b85fb245de1ceff976571085dd8cb6f 1710751 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769672/PAI001.A1.A2.TF.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769672/PAI001.A1.A2.TF.bam.bai +PLM001_TF half ds n/a SAMEA114211459 PRJEB51863 ERR11769673 PLM001.A ERS16192144 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PLM001.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/073/ERR11769673/ERR11769673.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/073/ERR11769673/ERR11769673.fastq.gz 41175528 dc19fe55523f1a15fa99f04357500d09 1257167 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769673/PLM001.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769673/PLM001.A0101.TF1.1.bam.bai +CBE003_MT half ds n/a SAMEA114211430 PRJEB51863 ERR11770483 CBE003.A ERS16192115 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CBE003.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/083/ERR11770483/ERR11770483.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/083/ERR11770483/ERR11770483.fastq.gz 129048 3da1fe7955be7318db60dec3c205708e 5442 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770483/CBE003.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770483/CBE003.A0101.MT1.1.bam.bai +EPS001_MT minus ds n/a SAMEA114211434 PRJEB51863 ERR11770487 EPS001.A ERS16192119 2023-07-30 2023-07-30 Illumina HiSeq 4000 PAIRED METAGENOMIC ILLUMINA EPS001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/087/ERR11770487/ERR11770487.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/087/ERR11770487/ERR11770487.fastq.gz 5128163 7a83c5cee035147420ce7e95d2f386bb 258367 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770487/EPS001.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770487/EPS001.A0101.MT1.1.bam.bai +JBT009_MT half ds n/a SAMEA114211443 PRJEB51863 ERR11770496 JBT009.A ERS16192128 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT009.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/096/ERR11770496/ERR11770496.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/096/ERR11770496/ERR11770496.fastq.gz 640323 07666246d604962744e4315fdfeabbde 29826 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770496/JBT009.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770496/JBT009.A0101.MT1.1.bam.bai +JBT018_MT half ds n/a SAMEA114211450 PRJEB51863 ERR11770503 JBT018.A ERS16192135 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT018.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/003/ERR11770503/ERR11770503.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/003/ERR11770503/ERR11770503.fastq.gz 676131 f277957ade7247860f2234838d7aaf0b 31268 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770503/JBT018.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770503/JBT018.A0101.MT1.1.bam.bai +JBT019_MT half ds n/a SAMEA114211451 PRJEB51863 ERR11770504 JBT019.A ERS16192136 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT019.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/004/ERR11770504/ERR11770504.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/004/ERR11770504/ERR11770504.fastq.gz 272672 28c936b6ed568281c6297db4221dc6a1 11794 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770504/JBT019.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770504/JBT019.A0101.MT1.1.bam.bai +JBT022_MT half ds n/a SAMEA114211454 PRJEB51863 ERR11770507 JBT022.A ERS16192139 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT022.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/007/ERR11770507/ERR11770507.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/007/ERR11770507/ERR11770507.fastq.gz 518915 6da17fd7d4b040a4ed76bf15f49f544f 23707 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770507/JBT022.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770507/JBT022.A0101.MT1.1.bam.bai +PAI001_MT half ds n/a SAMEA114211458 PRJEB51863 ERR11770511 PAI001.A ERS16192143 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PAI001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/011/ERR11770511/ERR11770511.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/011/ERR11770511/ERR11770511.fastq.gz 169173 217f17cd7fa8c39529013fe93ea3552b 7124 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770511/PAI001.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770511/PAI001.A0101.MT1.1.bam.bai +PLM001_MT half ds n/a SAMEA114211459 PRJEB51863 ERR11770512 PLM001.A ERS16192144 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PLM001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/012/ERR11770512/ERR11770512.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/012/ERR11770512/ERR11770512.fastq.gz 81071 0554e115099a49590436f9b10d5e3a3c 3372 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770512/PLM001.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770512/PLM001.A0101.MT1.1.bam.bai +CBE004_TF half ds n/a SAMEA114211431 PRJEB51863 ERR11769645 CBE004.A ERS16192116 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CBE004.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/045/ERR11769645/ERR11769645.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/045/ERR11769645/ERR11769645.fastq.gz 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fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/049/ERR11769649/ERR11769649.fastq.gz 43978995 219db96e0d590facdca40d572b83a0be 1236514 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769649/EPS002.A1.A2.TF.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769649/EPS002.A1.A2.TF.bam.bai +EPS003_TF half ds n/a SAMEA114211436 PRJEB51863 ERR11769650 EPS003.A ERS16192121 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA EPS003.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/050/ERR11769650/ERR11769650.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/050/ERR11769650/ERR11769650.fastq.gz 79777984 0377040ad01e98b113b10943b84589d7 2070340 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769650/EPS003.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769650/EPS003.A0101.TF1.1.bam.bai +EPS004_TF half ds n/a SAMEA114211437 PRJEB51863 ERR11769651 EPS004.A ERS16192122 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA EPS004.A0101.TF1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/051/ERR11769651/ERR11769651.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/051/ERR11769651/ERR11769651.fastq.gz 58585694 219180241b3b36c5c543d792bda06b5f 1603241 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769651/EPS004.A1.A2.TF.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769651/EPS004.A1.A2.TF.bam.bai +JBT012_TF half ds n/a SAMEA114211446 PRJEB51863 ERR11769660 JBT012.A ERS16192131 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT012.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/060/ERR11769660/ERR11769660.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/060/ERR11769660/ERR11769660.fastq.gz 147761973 7b0be3d21879e51f7565c0e8362e6a5c 4206845 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769660/JBT012.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769660/JBT012.A0101.TF1.1.bam.bai +JBT018_TF half ds n/a SAMEA114211450 PRJEB51863 ERR11769664 JBT018.A ERS16192135 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT018.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/064/ERR11769664/ERR11769664.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/064/ERR11769664/ERR11769664.fastq.gz 297152435 c68d8c0e7655b492d73f5b0cbafd8af6 8217879 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769664/JBT018.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769664/JBT018.A0101.TF1.1.bam.bai +JBT020_TF half ds n/a SAMEA114211452 PRJEB51863 ERR11769666 JBT020.A ERS16192137 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT020.A0101.TF1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/066/ERR11769666/ERR11769666.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/066/ERR11769666/ERR11769666.fastq.gz 36505093 49628501827a9cd8037185bd5e914271 1003891 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769666/JBT020.A1.A2.TF.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769666/JBT020.A1.A2.TF.bam.bai +JBT022_TF half ds n/a SAMEA114211454 PRJEB51863 ERR11769668 JBT022.A ERS16192139 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT022.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/068/ERR11769668/ERR11769668.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/068/ERR11769668/ERR11769668.fastq.gz 223120392 4fee6a1eaf69310beeb031136e0b3f52 6384490 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769668/JBT022.A0101.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769668/JBT022.A0101.TF1.1.bam.bai +SAM014_TF half ds n/a SAMEA114211460 PRJEB51863 ERR11769674 SAM014.A ERS16192145 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA SAM014.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/074/ERR11769674/ERR11769674.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/074/ERR11769674/ERR11769674.fastq.gz 39812695 5ec9586095e5a01bfdff5fb8af4c5391 1015585 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769674/SAM014.A1010.TF1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769674/SAM014.A1010.TF1.1.bam.bai +TDA002_TF minus ds n/a SAMEA114211461 PRJEB51863 ERR11769675 TDA002.A ERS16192146 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA TDA002.A0102.TF1.1_2_3 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/075/ERR11769675/ERR11769675.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/075/ERR11769675/ERR11769675.fastq.gz 31979683 a237472d8ac77356266f51a69bf79c1c 966976 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769675/TDA002.A1.A2.3.TF.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769675/TDA002.A1.A2.3.TF.bam.bai +VSM001_TF half ds n/a SAMEA114211462 PRJEB51863 ERR11769676 VSM001.A ERS16192147 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA VSM001.A0101.TF1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/076/ERR11769676/ERR11769676.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/076/ERR11769676/ERR11769676.fastq.gz 306300826 2a6ab92720d9d9dbf58761a7a6991af9 7571739 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769676/VSM001.A1.A2.TF.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11769676/VSM001.A1.A2.TF.bam.bai +CAP007_MT half ds n/a SAMEA114211429 PRJEB51863 ERR11770482 CAP007.A ERS16192114 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAP007.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/082/ERR11770482/ERR11770482.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/082/ERR11770482/ERR11770482.fastq.gz 261829 520ff4df06141963459e1db8eee5bf91 12501 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770482/CAP007.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770482/CAP007.A0101.MT1.1.bam.bai +EPS003_MT half ds n/a SAMEA114211436 PRJEB51863 ERR11770489 EPS003.A ERS16192121 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA EPS003.A0101.MT1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/089/ERR11770489/ERR11770489.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/089/ERR11770489/ERR11770489.fastq.gz 345562 45176c22681f0fa8d1019f4fcac2b4be 14781 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770489/EPS003.A0101.MT1.1_2.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770489/EPS003.A0101.MT1.1_2.bam.bai +EPS011_MT half ds n/a SAMEA114211439 PRJEB51863 ERR11770492 EPS011.A ERS16192124 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA EPS011.A0101.MT1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/092/ERR11770492/ERR11770492.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/092/ERR11770492/ERR11770492.fastq.gz 547737 0d3db6dae42e8feda9c7413ed5299ca9 25591 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770492/EPS011.A0101.MT1.1_2.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770492/EPS011.A0101.MT1.1_2.bam.bai +GA4002_MT half ds n/a SAMEA114211440 PRJEB51863 ERR11770493 GA4002.A ERS16192125 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GA4002.A0101.MT1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/093/ERR11770493/ERR11770493.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/093/ERR11770493/ERR11770493.fastq.gz 207727 8bfae95b524b84fd62fa247b96610079 9701 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770493/GA4002.A0101.MT1.1_2.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770493/GA4002.A0101.MT1.1_2.bam.bai +JBT002_MT half ds n/a SAMEA114211442 PRJEB51863 ERR11770495 JBT002.A ERS16192127 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT002.A0101.MT1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/095/ERR11770495/ERR11770495.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/095/ERR11770495/ERR11770495.fastq.gz 651670 0e54b13b383fcdb32cb9b7a93b5ce29d 45074 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770495/JBT002.A0101.MT1.1_2.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770495/JBT002.A0101.MT1.1_2.bam.bai +JBT011_MT half ds n/a SAMEA114211445 PRJEB51863 ERR11770498 JBT011.A ERS16192130 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT011.A0101.MT1.1_2 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/098/ERR11770498/ERR11770498.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/098/ERR11770498/ERR11770498.fastq.gz 349129 75f61fd9f00f66e44c11422deb8cb7d2 16948 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770498/JBT011.A0101.MT1.1_2.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770498/JBT011.A0101.MT1.1_2.bam.bai +JBT013_MT half ds n/a SAMEA114211447 PRJEB51863 ERR11770500 JBT013.A ERS16192132 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT013.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/000/ERR11770500/ERR11770500.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/000/ERR11770500/ERR11770500.fastq.gz 580413 927bd69df049f54b9e65dd2f25f78149 26455 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770500/JBT013.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770500/JBT013.A0101.MT1.1.bam.bai +JBT014_MT half ds n/a SAMEA114211448 PRJEB51863 ERR11770501 JBT014.A ERS16192133 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT014.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/001/ERR11770501/ERR11770501.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/001/ERR11770501/ERR11770501.fastq.gz 170581 f466138c591ecfcf979818a192636d28 7203 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770501/JBT014.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770501/JBT014.A0101.MT1.1.bam.bai +JBT021_MT half ds n/a SAMEA114211453 PRJEB51863 ERR11770506 JBT021.A ERS16192138 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT021.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/006/ERR11770506/ERR11770506.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/006/ERR11770506/ERR11770506.fastq.gz 556721 8e732ab850ae0c08372e1cded04ed4f8 25457 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770506/JBT021.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770506/JBT021.A0101.MT1.1.bam.bai +JBT026_MT half ds n/a SAMEA114211457 PRJEB51863 ERR11770510 JBT026.A ERS16192142 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA JBT026.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/010/ERR11770510/ERR11770510.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/010/ERR11770510/ERR11770510.fastq.gz 495645 51d20a7dad7e8ca0bc49ce6df211e84b 22734 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770510/JBT026.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770510/JBT026.A0101.MT1.1.bam.bai +VSM001_MT half ds n/a SAMEA114211462 PRJEB51863 ERR11770515 VSM001.A ERS16192147 2023-07-30 2023-07-30 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA VSM001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/015/ERR11770515/ERR11770515.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR117/015/ERR11770515/ERR11770515.fastq.gz 604317 055cb5e6c631c4bdcbebf0159f42f9a3 31047 ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770515/VSM001.A0101.MT1.1.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR117/ERR11770515/VSM001.A0101.MT1.1.bam.bai diff --git a/packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.tsv b/packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.tsv new file mode 100644 index 0000000..a8f3f2d --- /dev/null +++ b/packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.tsv @@ -0,0 +1,69 @@ +Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_Treatment R1 R2 BAM R1_target_file R2_target_file +CBE003_TF CBE003_TF_CBE003.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CBE003_TF_CBE003.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769644.fastq.gz NA +CUB002_TF CUB002_TF_CUB002.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CUB002_TF_CUB002.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769646.fastq.gz NA +GA4002_TF GA4002_TF_GA4002.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half /GA4002_TF_GA4002.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769654.fastq.gz NA +JBT009_TF JBT009_TF_JBT009.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT009_TF_JBT009.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769657.fastq.gz NA +JBT011_TF JBT011_TF_JBT011.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half /JBT011_TF_JBT011.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769659.fastq.gz NA +JBT015_TF JBT015_TF_JBT015.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT015_TF_JBT015.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769663.fastq.gz NA +JBT025_TF JBT025_TF_JBT025.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT025_TF_JBT025.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769670.fastq.gz NA +JBT026_TF JBT026_TF_JBT026.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT026_TF_JBT026.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769671.fastq.gz NA +CBE004_MT CBE004_MT_CBE004.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CBE004_MT_CBE004.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770484.fastq.gz NA +CUB002_MT CUB002_MT_CUB002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CUB002_MT_CUB002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770485.fastq.gz NA +CUB008_MT CUB008_MT_CUB008.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CUB008_MT_CUB008.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770486.fastq.gz NA +EPS002_MT EPS002_MT_EPS002.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half /EPS002_MT_EPS002.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770488.fastq.gz NA +EPS004_MT EPS004_MT_EPS004.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half /EPS004_MT_EPS004.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770490.fastq.gz NA +EPS005_MT EPS005_MT_EPS005.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half /EPS005_MT_EPS005.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770491.fastq.gz NA +JBT001_MT JBT001_MT_JBT001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT001_MT_JBT001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770494.fastq.gz NA +JBT010_MT JBT010_MT_JBT010.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT010_MT_JBT010.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770497.fastq.gz NA +JBT012_MT JBT012_MT_JBT012.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT012_MT_JBT012.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770499.fastq.gz NA +JBT015_MT JBT015_MT_JBT015.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT015_MT_JBT015.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770502.fastq.gz NA +JBT020_MT JBT020_MT_JBT020.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half /JBT020_MT_JBT020.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770505.fastq.gz NA +JBT023_MT JBT023_MT_JBT023.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT023_MT_JBT023.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770508.fastq.gz NA +JBT025_MT JBT025_MT_JBT025.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT025_MT_JBT025.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770509.fastq.gz NA +SAM014_MT SAM014_MT_SAM014.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /SAM014_MT_SAM014.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770513.fastq.gz NA +TDA002_MT TDA002_MT_TDA002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double none /TDA002_MT_TDA002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770514.fastq.gz NA +CAP007_TF CAP007_TF_CAP007.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half /CAP007_TF_CAP007.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769643.fastq.gz NA +EPS001_TF EPS001_TF_EPS001.A0102.TF1.1 1 4 SE Homo sapiens (modern human) double half /EPS001_TF_EPS001.A0102.TF1.1_L1_R1.fastq.gz NA NA ERR11769648.fastq.gz NA +EPS005_TF EPS005_TF_EPS005.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /EPS005_TF_EPS005.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769652.fastq.gz NA +EPS011_TF EPS011_TF_EPS011.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half /EPS011_TF_EPS011.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769653.fastq.gz NA +JBT001_TF JBT001_TF_JBT001.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT001_TF_JBT001.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769655.fastq.gz NA +JBT002_TF JBT002_TF_JBT002.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT002_TF_JBT002.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769656.fastq.gz NA +JBT010_TF JBT010_TF_JBT010.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT010_TF_JBT010.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769658.fastq.gz NA +JBT013_TF JBT013_TF_JBT013.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT013_TF_JBT013.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769661.fastq.gz NA +JBT014_TF JBT014_TF_JBT014.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT014_TF_JBT014.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769662.fastq.gz NA +JBT019_TF JBT019_TF_JBT019.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT019_TF_JBT019.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769665.fastq.gz NA +JBT021_TF JBT021_TF_JBT021.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT021_TF_JBT021.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769667.fastq.gz NA +JBT023_TF JBT023_TF_JBT023.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT023_TF_JBT023.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769669.fastq.gz NA +PAI001_TF PAI001_TF_PAI001.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half /PAI001_TF_PAI001.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769672.fastq.gz NA +PLM001_TF PLM001_TF_PLM001.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PLM001_TF_PLM001.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769673.fastq.gz NA +CBE003_MT CBE003_MT_CBE003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CBE003_MT_CBE003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770483.fastq.gz NA +EPS001_MT EPS001_MT_EPS001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double none /EPS001_MT_EPS001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770487.fastq.gz NA +JBT009_MT JBT009_MT_JBT009.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT009_MT_JBT009.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770496.fastq.gz NA +JBT018_MT JBT018_MT_JBT018.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT018_MT_JBT018.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770503.fastq.gz NA +JBT019_MT JBT019_MT_JBT019.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT019_MT_JBT019.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770504.fastq.gz NA +JBT022_MT JBT022_MT_JBT022.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT022_MT_JBT022.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770507.fastq.gz NA +PAI001_MT PAI001_MT_PAI001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PAI001_MT_PAI001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770511.fastq.gz NA +PLM001_MT PLM001_MT_PLM001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PLM001_MT_PLM001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770512.fastq.gz NA +CBE004_TF CBE004_TF_CBE004.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CBE004_TF_CBE004.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769645.fastq.gz NA +CUB008_TF CUB008_TF_CUB008.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half /CUB008_TF_CUB008.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769647.fastq.gz NA +EPS002_TF EPS002_TF_EPS002.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half /EPS002_TF_EPS002.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769649.fastq.gz NA +EPS003_TF EPS003_TF_EPS003.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /EPS003_TF_EPS003.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769650.fastq.gz NA +EPS004_TF EPS004_TF_EPS004.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half /EPS004_TF_EPS004.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769651.fastq.gz NA +JBT012_TF JBT012_TF_JBT012.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT012_TF_JBT012.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769660.fastq.gz NA +JBT018_TF JBT018_TF_JBT018.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT018_TF_JBT018.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769664.fastq.gz NA +JBT020_TF JBT020_TF_JBT020.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half /JBT020_TF_JBT020.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769666.fastq.gz NA +JBT022_TF JBT022_TF_JBT022.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /JBT022_TF_JBT022.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769668.fastq.gz NA +SAM014_TF SAM014_TF_SAM014.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /SAM014_TF_SAM014.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769674.fastq.gz NA +TDA002_TF TDA002_TF_TDA002.A0102.TF1.1_2_3 1 4 SE Homo sapiens (modern human) double none /TDA002_TF_TDA002.A0102.TF1.1_2_3_L1_R1.fastq.gz NA NA ERR11769675.fastq.gz NA +VSM001_TF VSM001_TF_VSM001.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half /VSM001_TF_VSM001.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769676.fastq.gz NA +CAP007_MT CAP007_MT_CAP007.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAP007_MT_CAP007.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770482.fastq.gz NA +EPS003_MT EPS003_MT_EPS003.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half /EPS003_MT_EPS003.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770489.fastq.gz NA +EPS011_MT EPS011_MT_EPS011.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half /EPS011_MT_EPS011.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770492.fastq.gz NA +GA4002_MT GA4002_MT_GA4002.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half /GA4002_MT_GA4002.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770493.fastq.gz NA +JBT002_MT JBT002_MT_JBT002.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half /JBT002_MT_JBT002.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770495.fastq.gz NA +JBT011_MT JBT011_MT_JBT011.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half /JBT011_MT_JBT011.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770498.fastq.gz NA +JBT013_MT JBT013_MT_JBT013.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT013_MT_JBT013.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770500.fastq.gz NA +JBT014_MT JBT014_MT_JBT014.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT014_MT_JBT014.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770501.fastq.gz NA +JBT021_MT JBT021_MT_JBT021.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT021_MT_JBT021.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770506.fastq.gz NA +JBT026_MT JBT026_MT_JBT026.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /JBT026_MT_JBT026.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770510.fastq.gz NA +VSM001_MT VSM001_MT_VSM001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /VSM001_MT_VSM001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770515.fastq.gz NA diff --git a/packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.tsv_patch.sh b/packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.tsv_patch.sh new file mode 100755 index 0000000..a73f9af --- /dev/null +++ b/packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.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/2023_Ferraz_NatureEcologyEvolution/script_versions.txt b/packages/2023_Ferraz_NatureEcologyEvolution/script_versions.txt new file mode 100644 index 0000000..7a83b10 --- /dev/null +++ b/packages/2023_Ferraz_NatureEcologyEvolution/script_versions.txt @@ -0,0 +1,2 @@ +create_eager_input.sh: 0.2.1dev +source_me.sh for initial TSV: 0.2.3dev