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Update: 2021_PattersonNature & 2020_Margaryan_Viking. Fix eof of SSFs #27

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Update: 2021_PattersonNature & 2020_Margaryan_Viking. Fix eof of SSFs #27

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0f00340
Add new line at EOF
TCLamnidis Apr 24, 2024
3e55777
Add new line at EOF
TCLamnidis Apr 24, 2024
21b09dc
[automated] Create package recipe from SSF files
Apr 24, 2024
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2 changes: 1 addition & 1 deletion packages/2020_Margaryan_Viking/2020_Margaryan_Viking.config
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Original file line number Diff line number Diff line change
@@ -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
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Suggested change
minotaur_release='0.3.0dev' // The release tag of the poseidon-eager repository used for processing and config file retrieval
minotaur_release='0.2.1' // The release tag of the poseidon-eager repository used for processing and config file retrieval

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Dont change version from already processed stuff to avoid rerunning

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"
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2 changes: 1 addition & 1 deletion packages/2020_Margaryan_Viking/2020_Margaryan_Viking.ssf
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Expand Up @@ -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
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
1 change: 1 addition & 0 deletions packages/2020_Margaryan_Viking/2020_Margaryan_Viking.tsv
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Expand Up @@ -440,3 +440,4 @@ VK536 VK536_unspecified 1 4 SE Homo sapiens (modern human) double none <PATH_TO_
VK538 VK538_unspecified 1 4 SE Homo sapiens (modern human) double none <PATH_TO_DATA>/VK538_unspecified_L1_R1.fastq.gz NA NA ERR4059899.fastq.gz NA
VK540 VK540_unspecified 1 4 SE Homo sapiens (modern human) double none <PATH_TO_DATA>/VK540_unspecified_L1_R1.fastq.gz NA NA ERR4059901.fastq.gz NA
VK543 VK543_unspecified 1 4 SE Homo sapiens (modern human) double none <PATH_TO_DATA>/VK543_unspecified_L1_R1.fastq.gz NA NA ERR4059904.fastq.gz NA
VK582 VK582_unspecified 1 4 SE Homo sapiens (modern human) double none <PATH_TO_DATA>/VK582_unspecified_L1_R1.fastq.gz NA NA ERR4059918.fastq.gz NA
18 changes: 10 additions & 8 deletions packages/2021_PattersonNature/2021_PattersonNature.config
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Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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)"

/*
Expand All @@ -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
*/
}
2 changes: 1 addition & 1 deletion packages/2021_PattersonNature/2021_PattersonNature.ssf
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Expand Up @@ -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.
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.
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