diff --git a/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.config b/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.config index 57c4b92..ca10f8b 100644 --- a/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.config +++ b/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.config @@ -1,5 +1,5 @@ // Keep track of config versions -minotaur_release='0.2.1' // The release tag of the poseidon-eager repository used for processing and config file retrieval +minotaur_release='0.3.0dev' // 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" diff --git a/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.ssf b/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.ssf index 6be8fbd..234bcc9 100644 --- a/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.ssf +++ b/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.ssf @@ -440,4 +440,4 @@ VK536 minus ds n/a ERR4059897 PRJEB37976 SAMEA6800259 VK536 ERS4527920 2020-09-1 VK538 minus ds n/a ERR4059899 PRJEB37976 SAMEA6800261 VK538 ERS4527922 2020-09-14 2020-04-23 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/009/ERR4059899/ERR4059899.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR405/009/ERR4059899/ERR4059899.fastq.gz 2809058851 f79c90b011afabc5d40d2cd6bfd0e1ac 62002854 ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059899/VK538.final.bam VK540 minus ds n/a ERR4059901 PRJEB37976 SAMEA6800263 VK540 ERS4527924 2020-09-14 2020-04-23 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/001/ERR4059901/ERR4059901.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR405/001/ERR4059901/ERR4059901.fastq.gz 1925286813 76af67a1c53dcea3b9c8f3f5420e14df 40952665 ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059901/VK540.final.bam VK543 minus ds n/a ERR4059904 PRJEB37976 SAMEA6800266 VK543 ERS4527927 2020-09-14 2020-04-23 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/004/ERR4059904/ERR4059904.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR405/004/ERR4059904/ERR4059904.fastq.gz 2175749580 055842d9afe961dfd05ac1a85388042a 44116249 ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059904/VK543.final.bam -VK582 minus ds n/a ERR4059918 PRJEB37976 SAMEA6800280 VK582 ERS4527941 2020-09-14 2020-04-23 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/008/ERR4059918/ERR4059918.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR405/008/ERR4059918/ERR4059918.fastq.gz 296111788 3503e67fa86929f06889f275b5ec7cc3 5284087 ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059918/VK582.final.bam \ No newline at end of file +VK582 minus ds n/a ERR4059918 PRJEB37976 SAMEA6800280 VK582 ERS4527941 2020-09-14 2020-04-23 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/008/ERR4059918/ERR4059918.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR405/008/ERR4059918/ERR4059918.fastq.gz 296111788 3503e67fa86929f06889f275b5ec7cc3 5284087 ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059918/VK582.final.bam diff --git a/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.tsv b/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.tsv index b24f06a..3780152 100644 --- a/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.tsv +++ b/packages/2020_Margaryan_Viking/2020_Margaryan_Viking.tsv @@ -440,3 +440,4 @@ VK536 VK536_unspecified 1 4 SE Homo sapiens (modern human) double none /VK538_unspecified_L1_R1.fastq.gz NA NA ERR4059899.fastq.gz NA VK540 VK540_unspecified 1 4 SE Homo sapiens (modern human) double none /VK540_unspecified_L1_R1.fastq.gz NA NA ERR4059901.fastq.gz NA VK543 VK543_unspecified 1 4 SE Homo sapiens (modern human) double none /VK543_unspecified_L1_R1.fastq.gz NA NA ERR4059904.fastq.gz NA +VK582 VK582_unspecified 1 4 SE Homo sapiens (modern human) double none /VK582_unspecified_L1_R1.fastq.gz NA NA ERR4059918.fastq.gz NA diff --git a/packages/2021_PattersonNature/2021_PattersonNature.config b/packages/2021_PattersonNature/2021_PattersonNature.config index 229a3c2..ca10f8b 100644 --- a/packages/2021_PattersonNature/2021_PattersonNature.config +++ b/packages/2021_PattersonNature/2021_PattersonNature.config @@ -1,6 +1,8 @@ // Keep track of config versions -config_template_version='0.2.0dev' -package_config_version='0.2.0dev' +minotaur_release='0.3.0dev' // 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 @@ -12,17 +14,17 @@ package_config_version='0.2.0dev' // from processing with the Minotaur workflow processing from the contents of a // single file. -// Load configuration profiles -includeConfig "../../conf/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA -includeConfig "../../conf/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing. +// 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 '../../conf/CaptureType_profiles/1240K.config' +includeConfig "${minotaur_config_base}/CaptureType_profiles/1240K.config" params { // Keep track of config file versions used when processing - config_profile_description = "${config_profile_description}\nconfig_template_version: ${config_template_version}\npackage_config_version: ${package_config_version}" + config_profile_description = "${config_profile_description}\n - config_template_version: ${config_template_version}\n - package_config_version: ${package_config_version}" config_profile_contact = "Thiseas C. Lamnidis (@TCLamnidis)" /* @@ -34,6 +36,6 @@ params { https://nf-co.re/eager/2.4.6/parameters You can see the default values for parameters within poseidon-eager at: - https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Poseidon.config + https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config */ } diff --git a/packages/2021_PattersonNature/2021_PattersonNature.ssf b/packages/2021_PattersonNature/2021_PattersonNature.ssf index 1fed176..f8edbc0 100644 --- a/packages/2021_PattersonNature/2021_PattersonNature.ssf +++ b/packages/2021_PattersonNature/2021_PattersonNature.ssf @@ -1670,4 +1670,4 @@ SAMEA10555869 PRJEB47891 ERR7194607 I11148.MT I11148 ds half ERS8207855 2021-10- SAMEA10555870 PRJEB47891 ERR7194608 I11149 I11149 ds half ERS8207856 2021-10-29 2021-10-29 Illumina HiSeq X SINGLE GENOMIC ILLUMINA ERS8207856 OTHER fasp.sra.ebi.ac.uk:/vol1/fastq/ERR719/008/ERR7194608/ERR7194608.fastq.gz 597900547 a791027d05697c47d7f8a9d29d0095a2 ftp.sra.ebi.ac.uk/vol1/fastq/ERR719/008/ERR7194608/ERR7194608.fastq.gz 19810419 ftp.sra.ebi.ac.uk/vol1/run/ERR719/ERR7194608/I11149.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR719/ERR7194608/I11149.bam.bai Sample information inferred from BAM name, cross-referenced with supplement. SAMEA10555871 PRJEB47891 ERR7194609 I11149.MT I11149 ds half ERS8207857 2021-10-29 2021-10-29 Illumina HiSeq X SINGLE GENOMIC ILLUMINA ERS8207857 OTHER fasp.sra.ebi.ac.uk:/vol1/fastq/ERR719/009/ERR7194609/ERR7194609.fastq.gz 8705353 a94e9119164445666c200cb9f7fd82a4 ftp.sra.ebi.ac.uk/vol1/fastq/ERR719/009/ERR7194609/ERR7194609.fastq.gz 429692 ftp.sra.ebi.ac.uk/vol1/run/ERR719/ERR7194609/I11149.MT.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR719/ERR7194609/I11149.MT.bam.bai Sample information inferred from BAM name, cross-referenced with supplement. SAMEA10555872 PRJEB47891 ERR7194610 I11150 I11150 ds half ERS8207858 2021-10-29 2021-10-29 Illumina HiSeq X SINGLE GENOMIC ILLUMINA ERS8207858 OTHER fasp.sra.ebi.ac.uk:/vol1/fastq/ERR719/000/ERR7194610/ERR7194610.fastq.gz 536012503 f4cf4975f541ff83097f553fdefa25c5 ftp.sra.ebi.ac.uk/vol1/fastq/ERR719/000/ERR7194610/ERR7194610.fastq.gz 17887817 ftp.sra.ebi.ac.uk/vol1/run/ERR719/ERR7194610/I11150.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR719/ERR7194610/I11150.bam.bai Sample information inferred from BAM name, cross-referenced with supplement. -SAMEA10555873 PRJEB47891 ERR7194611 I11150.ΜΤ I11150 ds half ERS8207859 2021-10-29 2021-10-29 Illumina HiSeq X SINGLE GENOMIC ILLUMINA ERS8207859 OTHER fasp.sra.ebi.ac.uk:/vol1/fastq/ERR719/001/ERR7194611/ERR7194611.fastq.gz 5612381 ee64c8deac02304d1d05b988298792da ftp.sra.ebi.ac.uk/vol1/fastq/ERR719/001/ERR7194611/ERR7194611.fastq.gz 282641 ftp.sra.ebi.ac.uk/vol1/run/ERR719/ERR7194611/I11150.MT.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR719/ERR7194611/I11150.MT.bam.bai Sample information inferred from BAM name, cross-referenced with supplement. \ No newline at end of file +SAMEA10555873 PRJEB47891 ERR7194611 I11150.ΜΤ I11150 ds half ERS8207859 2021-10-29 2021-10-29 Illumina HiSeq X SINGLE GENOMIC ILLUMINA ERS8207859 OTHER fasp.sra.ebi.ac.uk:/vol1/fastq/ERR719/001/ERR7194611/ERR7194611.fastq.gz 5612381 ee64c8deac02304d1d05b988298792da ftp.sra.ebi.ac.uk/vol1/fastq/ERR719/001/ERR7194611/ERR7194611.fastq.gz 282641 ftp.sra.ebi.ac.uk/vol1/run/ERR719/ERR7194611/I11150.MT.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR719/ERR7194611/I11150.MT.bam.bai Sample information inferred from BAM name, cross-referenced with supplement. diff --git a/packages/2021_PattersonNature/2021_PattersonNature.tsv b/packages/2021_PattersonNature/2021_PattersonNature.tsv index 0b5c617..0ba9d41 100644 --- a/packages/2021_PattersonNature/2021_PattersonNature.tsv +++ b/packages/2021_PattersonNature/2021_PattersonNature.tsv @@ -253,7 +253,6 @@ I13714 I13714_ERS8208145 1 4 SE Homo sapiens (modern human) double half /I13713_ERS8208143_L1_R1.fastq.gz NA NA ERR7194848.fastq.gz NA I13711 I13711_ERS8208139 1 4 SE Homo sapiens (modern human) double half /I13711_ERS8208139_L1_R1.fastq.gz NA NA ERR7194844.fastq.gz NA I1389 I1389_ERS8208234 1 4 SE Homo sapiens (modern human) double half /I1389_ERS8208234_L1_R1.fastq.gz NA NA ERR7194939.fastq.gz NA -I1389 I1389_ERS8208233 1 4 SE Homo sapiens (modern human) double half /I1389_ERS8208233_L1_R1.fastq.gz NA NA 0 1 I14192 I14192_ERS8208274 1 4 SE Homo sapiens (modern human) double half /I14192_ERS8208274_L1_R1.fastq.gz NA NA ERR7194979.fastq.gz NA I15045 I15045_ERS8208427 1 4 SE Homo sapiens (modern human) double half /I15045_ERS8208427_L1_R1.fastq.gz NA NA ERR7195132.fastq.gz NA I14190 I14190_ERS8208270 1 4 SE Homo sapiens (modern human) double half /I14190_ERS8208270_L1_R1.fastq.gz NA NA ERR7194975.fastq.gz NA @@ -281,7 +280,6 @@ I14188 I14188_ERS8208265 1 4 SE Homo sapiens (modern human) double half /I14191_ERS8208272_L1_R1.fastq.gz NA NA ERR7194977.fastq.gz NA I13890 I13890_ERS8208219 1 4 SE Homo sapiens (modern human) double half /I13890_ERS8208219_L1_R1.fastq.gz NA NA ERR7194924.fastq.gz NA I13795 I13795_ERS8208209 1 4 SE Homo sapiens (modern human) double half /I13795_ERS8208209_L1_R1.fastq.gz NA NA ERR7194914.fastq.gz NA -I1391 I1391_ERS8208235 1 4 SE Homo sapiens (modern human) double half /I1391_ERS8208235_L1_R1.fastq.gz NA NA 0 1 I13898 I13898_ERS8208229 1 4 SE Homo sapiens (modern human) double half /I13898_ERS8208229_L1_R1.fastq.gz NA NA ERR7194934.fastq.gz NA I13899 I13899_ERS8208232 1 4 SE Homo sapiens (modern human) double half /I13899_ERS8208232_L1_R1.fastq.gz NA NA ERR7194937.fastq.gz NA I13897 I13897_ERS8208228 1 4 SE Homo sapiens (modern human) double half /I13897_ERS8208228_L1_R1.fastq.gz NA NA ERR7194933.fastq.gz NA @@ -750,7 +748,6 @@ I16612 I16612_ERS8208683 1 4 SE Homo sapiens (modern human) double half /I11154_ERS8207914_L1_R1.fastq.gz NA NA ERR7194619.fastq.gz NA I11156 I11156_ERS8207915 1 4 SE Homo sapiens (modern human) double half /I11156_ERS8207915_L1_R1.fastq.gz NA NA ERR7194620.fastq.gz NA I11156 I11156_ERS8207916 1 4 SE Homo sapiens (modern human) double half /I11156_ERS8207916_L1_R1.fastq.gz NA NA ERR7194621.fastq.gz NA -I11158 I11158_ERS8207917 1 4 SE Homo sapiens (modern human) double half /I11158_ERS8207917_L1_R1.fastq.gz NA NA 0 1 I11158 I11158_ERS8207918 1 4 SE Homo sapiens (modern human) double half /I11158_ERS8207918_L1_R1.fastq.gz NA NA ERR7194623.fastq.gz NA I12097_ss I12097_ss_ERS8207978_ss 1 4 SE Homo sapiens (modern human) single half /I12097_ss_ERS8207978_ss_L1_R1.fastq.gz NA NA ERR7194683.fastq.gz NA I17139_ss I17139_ss_ERS8208715_ss 1 4 SE Homo sapiens (modern human) single half /I17139_ss_ERS8208715_ss_L1_R1.fastq.gz NA NA ERR7195420.fastq.gz NA @@ -761,12 +758,10 @@ I17017 I17017_ERS8208711 1 4 SE Homo sapiens (modern human) double half /I17143_ss_ERS8208717_ss_L1_R1.fastq.gz NA NA ERR7195422.fastq.gz NA I17139_ss I17139_ss_ERS8208716_ss 1 4 SE Homo sapiens (modern human) single half /I17139_ss_ERS8208716_ss_L1_R1.fastq.gz NA NA ERR7195421.fastq.gz NA I12098 I12098_ERS8207979 1 4 SE Homo sapiens (modern human) double half /I12098_ERS8207979_L1_R1.fastq.gz NA NA ERR7194684.fastq.gz NA -I11159 I11159_ERS8207919 1 4 SE Homo sapiens (modern human) double half /I11159_ERS8207919_L1_R1.fastq.gz NA NA 0 1 I12098 I12098_ERS8207980 1 4 SE Homo sapiens (modern human) double half /I12098_ERS8207980_L1_R1.fastq.gz NA NA ERR7194685.fastq.gz NA I11152 I11152_ERS8207909 1 4 SE Homo sapiens (modern human) double half /I11152_ERS8207909_L1_R1.fastq.gz NA NA ERR7194614.fastq.gz NA I11151 I11151_ERS8207908 1 4 SE Homo sapiens (modern human) double half /I11151_ERS8207908_L1_R1.fastq.gz NA NA ERR7194613.fastq.gz NA I11159 I11159_ERS8207920 1 4 SE Homo sapiens (modern human) double half /I11159_ERS8207920_L1_R1.fastq.gz NA NA ERR7194625.fastq.gz NA -I11160 I11160_ERS8207921 1 4 SE Homo sapiens (modern human) double half /I11160_ERS8207921_L1_R1.fastq.gz NA NA 0 1 I11160 I11160_ERS8207922 1 4 SE Homo sapiens (modern human) double half /I11160_ERS8207922_L1_R1.fastq.gz NA NA ERR7194627.fastq.gz NA I11629 I11629_ERS8207923 1 4 SE Homo sapiens (modern human) double half /I11629_ERS8207923_L1_R1.fastq.gz NA NA ERR7194628.fastq.gz NA I12099 I12099_ERS8207981 1 4 SE Homo sapiens (modern human) double half /I12099_ERS8207981_L1_R1.fastq.gz NA NA ERR7194686.fastq.gz NA @@ -1353,13 +1348,9 @@ I23995 I23995_ERS8209257 1 4 SE Homo sapiens (modern human) double half /I23995_ERS8209258_L1_R1.fastq.gz NA NA ERR7195963.fastq.gz NA I23996 I23996_ERS8209259 1 4 SE Homo sapiens (modern human) double half /I23996_ERS8209259_L1_R1.fastq.gz NA NA ERR7195964.fastq.gz NA I23996 I23996_ERS8209260 1 4 SE Homo sapiens (modern human) double half /I23996_ERS8209260_L1_R1.fastq.gz NA NA ERR7195965.fastq.gz NA -I2405 I2405_ERS8209261 1 4 SE Homo sapiens (modern human) double half /I2405_ERS8209261_L1_R1.fastq.gz NA NA 0 1 I2405 I2405_ERS8209262 1 4 SE Homo sapiens (modern human) double half /I2405_ERS8209262_L1_R1.fastq.gz NA NA ERR7195967.fastq.gz NA -I2407 I2407_ERS8209263 1 4 SE Homo sapiens (modern human) double half /I2407_ERS8209263_L1_R1.fastq.gz NA NA 0 1 I2407 I2407_ERS8209264 1 4 SE Homo sapiens (modern human) double half /I2407_ERS8209264_L1_R1.fastq.gz NA NA ERR7195969.fastq.gz NA -I2413 I2413_ERS8209265 1 4 SE Homo sapiens (modern human) double half /I2413_ERS8209265_L1_R1.fastq.gz NA NA 0 1 I2413 I2413_ERS8209266 1 4 SE Homo sapiens (modern human) double half /I2413_ERS8209266_L1_R1.fastq.gz NA NA ERR7195971.fastq.gz NA -I2419 I2419_ERS8209267 1 4 SE Homo sapiens (modern human) double half /I2419_ERS8209267_L1_R1.fastq.gz NA NA 0 1 I2419 I2419_ERS8209268 1 4 SE Homo sapiens (modern human) double half /I2419_ERS8209268_L1_R1.fastq.gz NA NA ERR7195973.fastq.gz NA I24342 I24342_ERS8209269 1 4 SE Homo sapiens (modern human) double half /I24342_ERS8209269_L1_R1.fastq.gz NA NA ERR7195974.fastq.gz NA I24342 I24342_ERS8209270 1 4 SE Homo sapiens (modern human) double half /I24342_ERS8209270_L1_R1.fastq.gz NA NA ERR7195975.fastq.gz NA @@ -1367,7 +1358,6 @@ I24344 I24344_ERS8209271 1 4 SE Homo sapiens (modern human) double half /I24344_ERS8209272_L1_R1.fastq.gz NA NA ERR7195977.fastq.gz NA I24345 I24345_ERS8209273 1 4 SE Homo sapiens (modern human) double half /I24345_ERS8209273_L1_R1.fastq.gz NA NA ERR7195978.fastq.gz NA I24345 I24345_ERS8209274 1 4 SE Homo sapiens (modern human) double half /I24345_ERS8209274_L1_R1.fastq.gz NA NA ERR7195979.fastq.gz NA -I2435 I2435_ERS8209275 1 4 SE Homo sapiens (modern human) double half /I2435_ERS8209275_L1_R1.fastq.gz NA NA 0 1 I2435 I2435_ERS8209276 1 4 SE Homo sapiens (modern human) double half /I2435_ERS8209276_L1_R1.fastq.gz NA NA ERR7195981.fastq.gz NA I2446 I2446_ERS8209277 1 4 SE Homo sapiens (modern human) double half /I2446_ERS8209277_L1_R1.fastq.gz NA NA ERR7195982.fastq.gz NA I2446 I2446_ERS8209278 1 4 SE Homo sapiens (modern human) double half /I2446_ERS8209278_L1_R1.fastq.gz NA NA ERR7195983.fastq.gz NA @@ -1419,19 +1409,15 @@ I25525 I25525_ERS8209323 1 4 SE Homo sapiens (modern human) double half /I25525_ERS8209324_L1_R1.fastq.gz NA NA ERR7196029.fastq.gz NA I2565 I2565_ERS8209325 1 4 SE Homo sapiens (modern human) double half /I2565_ERS8209325_L1_R1.fastq.gz NA NA ERR7196030.fastq.gz NA I2565 I2565_ERS8209326 1 4 SE Homo sapiens (modern human) double half /I2565_ERS8209326_L1_R1.fastq.gz NA NA ERR7196031.fastq.gz NA -I2569 I2569_ERS8209327 1 4 SE Homo sapiens (modern human) double half /I2569_ERS8209327_L1_R1.fastq.gz NA NA 0 1 I2569 I2569_ERS8209328 1 4 SE Homo sapiens (modern human) double half /I2569_ERS8209328_L1_R1.fastq.gz NA NA ERR7196033.fastq.gz NA I2574 I2574_ERS8209329 1 4 SE Homo sapiens (modern human) double half /I2574_ERS8209329_L1_R1.fastq.gz NA NA ERR7196034.fastq.gz NA I2574 I2574_ERS8209330 1 4 SE Homo sapiens (modern human) double half /I2574_ERS8209330_L1_R1.fastq.gz NA NA ERR7196035.fastq.gz NA -I2575 I2575_ERS8209331 1 4 SE Homo sapiens (modern human) double half /I2575_ERS8209331_L1_R1.fastq.gz NA NA 0 1 I2575 I2575_ERS8209332 1 4 SE Homo sapiens (modern human) double half /I2575_ERS8209332_L1_R1.fastq.gz NA NA ERR7196037.fastq.gz NA I2598 I2598_ERS8209333 1 4 SE Homo sapiens (modern human) double half /I2598_ERS8209333_L1_R1.fastq.gz NA NA ERR7196038.fastq.gz NA I2598 I2598_ERS8209334 1 4 SE Homo sapiens (modern human) double half /I2598_ERS8209334_L1_R1.fastq.gz NA NA ERR7196039.fastq.gz NA I2611 I2611_ERS8209335 1 4 SE Homo sapiens (modern human) double half /I2611_ERS8209335_L1_R1.fastq.gz NA NA ERR7196040.fastq.gz NA I2611 I2611_ERS8209336 1 4 SE Homo sapiens (modern human) double half /I2611_ERS8209336_L1_R1.fastq.gz NA NA ERR7196041.fastq.gz NA -I2629 I2629_ERS8209337 1 4 SE Homo sapiens (modern human) double half /I2629_ERS8209337_L1_R1.fastq.gz NA NA 0 1 I2629 I2629_ERS8209338 1 4 SE Homo sapiens (modern human) double half /I2629_ERS8209338_L1_R1.fastq.gz NA NA ERR7196043.fastq.gz NA -I2656 I2656_ERS8209339 1 4 SE Homo sapiens (modern human) double half /I2656_ERS8209339_L1_R1.fastq.gz NA NA 0 1 I2656 I2656_ERS8209340 1 4 SE Homo sapiens (modern human) double half /I2656_ERS8209340_L1_R1.fastq.gz NA NA ERR7196045.fastq.gz NA I2658 I2658_ERS8209341 1 4 SE Homo sapiens (modern human) double half /I2658_ERS8209341_L1_R1.fastq.gz NA NA ERR7196046.fastq.gz NA I2658 I2658_ERS8209342 1 4 SE Homo sapiens (modern human) double half /I2658_ERS8209342_L1_R1.fastq.gz NA NA ERR7196047.fastq.gz NA @@ -1477,7 +1463,6 @@ I2695 I2695_ERS8209381 1 4 SE Homo sapiens (modern human) double half /I2695_ERS8209382_L1_R1.fastq.gz NA NA ERR7196087.fastq.gz NA I2696 I2696_ERS8209383 1 4 SE Homo sapiens (modern human) double half /I2696_ERS8209383_L1_R1.fastq.gz NA NA ERR7196088.fastq.gz NA I2696 I2696_ERS8209384 1 4 SE Homo sapiens (modern human) double half /I2696_ERS8209384_L1_R1.fastq.gz NA NA ERR7196089.fastq.gz NA -I2699 I2699_ERS8209385 1 4 SE Homo sapiens (modern human) double half /I2699_ERS8209385_L1_R1.fastq.gz NA NA 0 1 I2699 I2699_ERS8209386 1 4 SE Homo sapiens (modern human) double half /I2699_ERS8209386_L1_R1.fastq.gz NA NA ERR7196091.fastq.gz NA I27379 I27379_ERS8209387 1 4 SE Homo sapiens (modern human) double half /I27379_ERS8209387_L1_R1.fastq.gz NA NA ERR7196092.fastq.gz NA I27379 I27379_ERS8209388 1 4 SE Homo sapiens (modern human) double half /I27379_ERS8209388_L1_R1.fastq.gz NA NA ERR7196093.fastq.gz NA @@ -1493,11 +1478,9 @@ I27384 I27384_ERS8209397 1 4 SE Homo sapiens (modern human) double half /I27384_ERS8209398_L1_R1.fastq.gz NA NA ERR7196103.fastq.gz NA I27385 I27385_ERS8209399 1 4 SE Homo sapiens (modern human) double half /I27385_ERS8209399_L1_R1.fastq.gz NA NA ERR7196104.fastq.gz NA I27385 I27385_ERS8209400 1 4 SE Homo sapiens (modern human) double half /I27385_ERS8209400_L1_R1.fastq.gz NA NA ERR7196105.fastq.gz NA -I2796 I2796_ERS8209401 1 4 SE Homo sapiens (modern human) double half /I2796_ERS8209401_L1_R1.fastq.gz NA NA 0 1 I2796 I2796_ERS8209402 1 4 SE Homo sapiens (modern human) double half /I2796_ERS8209402_L1_R1.fastq.gz NA NA ERR7196107.fastq.gz NA I2799 I2799_ERS8209403 1 4 SE Homo sapiens (modern human) double half /I2799_ERS8209403_L1_R1.fastq.gz NA NA ERR7196108.fastq.gz NA I2799 I2799_ERS8209404 1 4 SE Homo sapiens (modern human) double half /I2799_ERS8209404_L1_R1.fastq.gz NA NA ERR7196109.fastq.gz NA -I2824 I2824_ERS8209405 1 4 SE Homo sapiens (modern human) double half /I2824_ERS8209405_L1_R1.fastq.gz NA NA 0 1 I2824 I2824_ERS8209406 1 4 SE Homo sapiens (modern human) double half /I2824_ERS8209406_L1_R1.fastq.gz NA NA ERR7196111.fastq.gz NA I2982 I2982_ERS8209407 1 4 SE Homo sapiens (modern human) double half /I2982_ERS8209407_L1_R1.fastq.gz NA NA ERR7196112.fastq.gz NA I2982 I2982_ERS8209408 1 4 SE Homo sapiens (modern human) double half /I2982_ERS8209408_L1_R1.fastq.gz NA NA ERR7196113.fastq.gz NA @@ -1511,7 +1494,6 @@ I3035 I3035_ERS8209415 1 4 SE Homo sapiens (modern human) double half /I3035_ERS8209416_L1_R1.fastq.gz NA NA ERR7196121.fastq.gz NA I3083 I3083_ERS8209417 1 4 SE Homo sapiens (modern human) double full /I3083_ERS8209417_L1_R1.fastq.gz NA NA ERR7196122.fastq.gz NA I3083 I3083_ERS8209418 1 4 SE Homo sapiens (modern human) double full /I3083_ERS8209418_L1_R1.fastq.gz NA NA ERR7196123.fastq.gz NA -I3137 I3137_ERS8209419 1 4 SE Homo sapiens (modern human) double half /I3137_ERS8209419_L1_R1.fastq.gz NA NA 0 1 I3137 I3137_ERS8209420 1 4 SE Homo sapiens (modern human) double half /I3137_ERS8209420_L1_R1.fastq.gz NA NA ERR7196125.fastq.gz NA I3139 I3139_ERS8209421 1 4 SE Homo sapiens (modern human) double half /I3139_ERS8209421_L1_R1.fastq.gz NA NA ERR7196126.fastq.gz NA I3139 I3139_ERS8209422 1 4 SE Homo sapiens (modern human) double half /I3139_ERS8209422_L1_R1.fastq.gz NA NA ERR7196127.fastq.gz NA @@ -1529,7 +1511,6 @@ I3567 I3567_ERS8209433 1 4 SE Homo sapiens (modern human) double half /I3567_ERS8209434_L1_R1.fastq.gz NA NA ERR7196139.fastq.gz NA I3568 I3568_ERS8209435 1 4 SE Homo sapiens (modern human) double half /I3568_ERS8209435_L1_R1.fastq.gz NA NA ERR7196140.fastq.gz NA I3568 I3568_ERS8209436 1 4 SE Homo sapiens (modern human) double half /I3568_ERS8209436_L1_R1.fastq.gz NA NA ERR7196141.fastq.gz NA -I4067 I4067_ERS8209437 1 4 SE Homo sapiens (modern human) double half /I4067_ERS8209437_L1_R1.fastq.gz NA NA 0 1 I4067 I4067_ERS8209438 1 4 SE Homo sapiens (modern human) double half /I4067_ERS8209438_L1_R1.fastq.gz NA NA ERR7196143.fastq.gz NA I4188 I4188_ERS8209439 1 4 SE Homo sapiens (modern human) double half /I4188_ERS8209439_L1_R1.fastq.gz NA NA ERR7196144.fastq.gz NA I4188 I4188_ERS8209440 1 4 SE Homo sapiens (modern human) double half /I4188_ERS8209440_L1_R1.fastq.gz NA NA ERR7196145.fastq.gz NA @@ -1547,9 +1528,7 @@ I5365 I5365_ERS8209451 1 4 SE Homo sapiens (modern human) double half /I5365_ERS8209452_L1_R1.fastq.gz NA NA ERR7196157.fastq.gz NA I5440 I5440_ERS8209453 1 4 SE Homo sapiens (modern human) double half /I5440_ERS8209453_L1_R1.fastq.gz NA NA ERR7196158.fastq.gz NA I5440 I5440_ERS8209454 1 4 SE Homo sapiens (modern human) double half /I5440_ERS8209454_L1_R1.fastq.gz NA NA ERR7196159.fastq.gz NA -I5471 I5471_ERS8209455 1 4 SE Homo sapiens (modern human) double half /I5471_ERS8209455_L1_R1.fastq.gz NA NA 0 1 I5471 I5471_ERS8209456 1 4 SE Homo sapiens (modern human) double half /I5471_ERS8209456_L1_R1.fastq.gz NA NA ERR7196161.fastq.gz NA -I5474 I5474_ERS8209457 1 4 SE Homo sapiens (modern human) double half /I5474_ERS8209457_L1_R1.fastq.gz NA NA 0 1 I5474 I5474_ERS8209458 1 4 SE Homo sapiens (modern human) double half /I5474_ERS8209458_L1_R1.fastq.gz NA NA ERR7196163.fastq.gz NA I5502 I5502_ERS8209459 1 4 SE Homo sapiens (modern human) double half /I5502_ERS8209459_L1_R1.fastq.gz NA NA ERR7196164.fastq.gz NA I5502 I5502_ERS8209460 1 4 SE Homo sapiens (modern human) double half /I5502_ERS8209460_L1_R1.fastq.gz NA NA ERR7196165.fastq.gz NA @@ -1601,23 +1580,14 @@ I7629 I7629_ERS8209505 1 4 SE Homo sapiens (modern human) double half /I7629_ERS8209506_L1_R1.fastq.gz NA NA ERR7196211.fastq.gz NA I7632 I7632_ERS8209507 1 4 SE Homo sapiens (modern human) double half /I7632_ERS8209507_L1_R1.fastq.gz NA NA ERR7196212.fastq.gz NA I7632 I7632_ERS8209508 1 4 SE Homo sapiens (modern human) double half /I7632_ERS8209508_L1_R1.fastq.gz NA NA ERR7196213.fastq.gz NA -I7950 I7950_ERS8209509 1 4 SE Homo sapiens (modern human) double half /I7950_ERS8209509_L1_R1.fastq.gz NA NA 0 1 I7950 I7950_ERS8209510 1 4 SE Homo sapiens (modern human) double half /I7950_ERS8209510_L1_R1.fastq.gz NA NA ERR7196215.fastq.gz NA -I7951 I7951_ERS8209511 1 4 SE Homo sapiens (modern human) double half /I7951_ERS8209511_L1_R1.fastq.gz NA NA 0 1 I7951 I7951_ERS8209512 1 4 SE Homo sapiens (modern human) double half /I7951_ERS8209512_L1_R1.fastq.gz NA NA ERR7196217.fastq.gz NA -I7952 I7952_ERS8209513 1 4 SE Homo sapiens (modern human) double half /I7952_ERS8209513_L1_R1.fastq.gz NA NA 0 1 I7952 I7952_ERS8209514 1 4 SE Homo sapiens (modern human) double half /I7952_ERS8209514_L1_R1.fastq.gz NA NA ERR7196219.fastq.gz NA -I7953 I7953_ERS8209515 1 4 SE Homo sapiens (modern human) double half /I7953_ERS8209515_L1_R1.fastq.gz NA NA 0 1 I7953 I7953_ERS8209516 1 4 SE Homo sapiens (modern human) double half /I7953_ERS8209516_L1_R1.fastq.gz NA NA ERR7196221.fastq.gz NA -I7958 I7958_ERS8209517 1 4 SE Homo sapiens (modern human) double half /I7958_ERS8209517_L1_R1.fastq.gz NA NA 0 1 I7958 I7958_ERS8209518 1 4 SE Homo sapiens (modern human) double half /I7958_ERS8209518_L1_R1.fastq.gz NA NA ERR7196223.fastq.gz NA -I7959 I7959_ERS8209519 1 4 SE Homo sapiens (modern human) double half /I7959_ERS8209519_L1_R1.fastq.gz NA NA 0 1 I7959 I7959_ERS8209520 1 4 SE Homo sapiens (modern human) double half /I7959_ERS8209520_L1_R1.fastq.gz NA NA ERR7196225.fastq.gz NA -I7960 I7960_ERS8209521 1 4 SE Homo sapiens (modern human) double half /I7960_ERS8209521_L1_R1.fastq.gz NA NA 0 1 I7960 I7960_ERS8209522 1 4 SE Homo sapiens (modern human) double half /I7960_ERS8209522_L1_R1.fastq.gz NA NA ERR7196227.fastq.gz NA -I7962 I7962_ERS8209523 1 4 SE Homo sapiens (modern human) double half /I7962_ERS8209523_L1_R1.fastq.gz NA NA 0 1 I7962 I7962_ERS8209524 1 4 SE Homo sapiens (modern human) double half /I7962_ERS8209524_L1_R1.fastq.gz NA NA ERR7196229.fastq.gz NA -I7963 I7963_ERS8209525 1 4 SE Homo sapiens (modern human) double half /I7963_ERS8209525_L1_R1.fastq.gz NA NA 0 1 I7963 I7963_ERS8209526 1 4 SE Homo sapiens (modern human) double half /I7963_ERS8209526_L1_R1.fastq.gz NA NA ERR7196231.fastq.gz NA I7964 I7964_ERS8209527 1 4 SE Homo sapiens (modern human) double half /I7964_ERS8209527_L1_R1.fastq.gz NA NA ERR7196232.fastq.gz NA I7964 I7964_ERS8209528 1 4 SE Homo sapiens (modern human) double half /I7964_ERS8209528_L1_R1.fastq.gz NA NA ERR7196233.fastq.gz NA @@ -1637,17 +1607,11 @@ I0525 I0525_ERS8207822 1 4 SE Homo sapiens (modern human) double half /I0525_ERS8207823_L1_R1.fastq.gz NA NA ERR7194575.fastq.gz NA I0527 I0527_ERS8207824 1 4 SE Homo sapiens (modern human) double half /I0527_ERS8207824_L1_R1.fastq.gz NA NA ERR7194576.fastq.gz NA I0527 I0527_ERS8207825 1 4 SE Homo sapiens (modern human) double half /I0527_ERS8207825_L1_R1.fastq.gz NA NA ERR7194577.fastq.gz NA -I10342 I10342_ERS8207826 1 4 SE Homo sapiens (modern human) double half /I10342_ERS8207826_L1_R1.fastq.gz NA NA 0 1 I10342 I10342_ERS8207827 1 4 SE Homo sapiens (modern human) double half /I10342_ERS8207827_L1_R1.fastq.gz NA NA ERR7194579.fastq.gz NA -I10343 I10343_ERS8207828 1 4 SE Homo sapiens (modern human) double half /I10343_ERS8207828_L1_R1.fastq.gz NA NA 0 1 I10343 I10343_ERS8207829 1 4 SE Homo sapiens (modern human) double half /I10343_ERS8207829_L1_R1.fastq.gz NA NA ERR7194581.fastq.gz NA -I10344 I10344_ERS8207830 1 4 SE Homo sapiens (modern human) double half /I10344_ERS8207830_L1_R1.fastq.gz NA NA 0 1 I10344 I10344_ERS8207831 1 4 SE Homo sapiens (modern human) double half /I10344_ERS8207831_L1_R1.fastq.gz NA NA ERR7194583.fastq.gz NA -I10345 I10345_ERS8207832 1 4 SE Homo sapiens (modern human) double half /I10345_ERS8207832_L1_R1.fastq.gz NA NA 0 1 I10345 I10345_ERS8207833 1 4 SE Homo sapiens (modern human) double half /I10345_ERS8207833_L1_R1.fastq.gz NA NA ERR7194585.fastq.gz NA -I10347 I10347_ERS8207834 1 4 SE Homo sapiens (modern human) double half /I10347_ERS8207834_L1_R1.fastq.gz NA NA 0 1 I10347 I10347_ERS8207835 1 4 SE Homo sapiens (modern human) double half /I10347_ERS8207835_L1_R1.fastq.gz NA NA ERR7194587.fastq.gz NA -I10348 I10348_ERS8207836 1 4 SE Homo sapiens (modern human) double half /I10348_ERS8207836_L1_R1.fastq.gz NA NA 0 1 I10348 I10348_ERS8207837 1 4 SE Homo sapiens (modern human) double half /I10348_ERS8207837_L1_R1.fastq.gz NA NA ERR7194589.fastq.gz NA I11033 I11033_ERS8207838 1 4 SE Homo sapiens (modern human) double half /I11033_ERS8207838_L1_R1.fastq.gz NA NA ERR7194590.fastq.gz NA I11033 I11033_ERS8207839 1 4 SE Homo sapiens (modern human) double half /I11033_ERS8207839_L1_R1.fastq.gz NA NA ERR7194591.fastq.gz NA @@ -1670,3 +1634,4 @@ I11148 I11148_ERS8207855 1 4 SE Homo sapiens (modern human) double half /I11149_ERS8207856_L1_R1.fastq.gz NA NA ERR7194608.fastq.gz NA I11149 I11149_ERS8207857 1 4 SE Homo sapiens (modern human) double half /I11149_ERS8207857_L1_R1.fastq.gz NA NA ERR7194609.fastq.gz NA I11150 I11150_ERS8207858 1 4 SE Homo sapiens (modern human) double half /I11150_ERS8207858_L1_R1.fastq.gz NA NA ERR7194610.fastq.gz NA +I11150 I11150_ERS8207859 1 4 SE Homo sapiens (modern human) double half /I11150_ERS8207859_L1_R1.fastq.gz NA NA ERR7194611.fastq.gz NA diff --git a/packages/2021_PattersonNature/2021_PattersonNature.tsv_patch.sh b/packages/2021_PattersonNature/2021_PattersonNature.tsv_patch.sh index 422e836..a73f9af 100755 --- a/packages/2021_PattersonNature/2021_PattersonNature.tsv_patch.sh +++ b/packages/2021_PattersonNature/2021_PattersonNature.tsv_patch.sh @@ -2,7 +2,7 @@ set -uo pipefail ## Pipefail, complain on new unassigned variables. ## Track the version of the TSV_patch template used -VERSION='0.2.0dev' +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 @@ -10,13 +10,13 @@ VERSION='0.2.0dev' ## TSV before running eager should be added below that in the form of bash ## commands to aid in reproducibility. -## usage tsv_patch.sh +## 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 $(dirname ${2})/../../scripts/source_me.sh ## Load helper functions +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='' diff --git a/packages/2021_PattersonNature/script_versions.txt b/packages/2021_PattersonNature/script_versions.txt index fc73d50..be6857b 100644 --- a/packages/2021_PattersonNature/script_versions.txt +++ b/packages/2021_PattersonNature/script_versions.txt @@ -1,2 +1,2 @@ -create_eager_input.sh: 0.2.0dev -source_me.sh for initial TSV: 0.2.0dev +create_eager_input.sh: 0.2.1dev +source_me.sh for initial TSV: 0.2.1dev