Merge pull request #226 from wtsi-npg/devel

release 51.10 prep

Changes

@@ -1,6 +1,22 @@
 LIST OF CHANGES
 ---------------
 
+ - Chained execution of RNA-SeQC to the vtfp/viv alignment cmd for RNA-Seq libraries only:
+     entries for qc check rna_seqc removed from central function and parallelisation.
+     code that created rna_seqc-specific directories has been removed as this is
+     now handled by the check itself using qc_out arg.
+ - remove GCLP-specific code and configuration files
+ - remove unused force_p4 attribute
+ - OLB analysis removed
+ - recalibration removed
+ - pb_cal_path and dif_files_path accessors disabled
+ - allow p4 stage 1 to analyse runs with different length reads
+ - illumina2bam function removed
+ - update p4 stage 2 (seq_alignment) warn rather than croak if multiple references for tag 0
+ - update p4 stage 2 (seq_alignment) to use bambi chrsplit instead of SplitBamByChromosomes.jar for Y-split runs
+ - pipeline scripts - redirect stderr output to the log to capture output from all
+   NPG and CPAN modules in one place
+
 release 51.9
  - p4stage2 speed-up by caching references
  - p4stage2 errors in getting a reference made fatal
@@ -20,6 +36,9 @@ release 51.8
 release 51.7
  - replaces the original log role with the one from DNAP utilities,
    which provides a Log4perl logger and some convenience methods.
+ - new signature for the sequencescape warehouse loader so that it uses
+   samplsheet LIMs driver at the analysis stage and ml_warehouse_fc_cache
+   LIMs driver at the archival stage
 
 release 51.6
  - test and code fixes to ensure problem-free tests under Perl 5.22.2

MANIFEST

@@ -11,23 +11,16 @@ bin/script_must_be_unique_runner
 Build.PL
 Changes
 data/config_files/function_list_central.yml
-data/config_files/function_list_central_gclp.yml
-data/config_files/function_list_central_olb.yml
 data/config_files/function_list_central_qc_run.yml
 data/config_files/function_list_post_qc_review.yml
-data/config_files/function_list_post_qc_review_gclp.yml
 data/config_files/general_values.ini
-data/config_files/illumina_pipeline.ini
 data/config_files/parallelisation.yml
-data/config_files/pb_cal_pipeline.ini
-lib/npg_pipeline/analysis/bustard4pbcb.pm
 lib/npg_pipeline/analysis/create_lane_tag_file.pm
 lib/npg_pipeline/analysis/FixConfigFiles.pm
-lib/npg_pipeline/analysis/harold_calibration_bam.pm
+lib/npg_pipeline/analysis/illumina_basecall_stats.pm
 lib/npg_pipeline/analysis/split_bam_by_tag.pm
 lib/npg_pipeline/archive/file/BamClusterCounts.pm
 lib/npg_pipeline/archive/file/generation.pm
-lib/npg_pipeline/archive/file/generation/illumina2bam.pm
 lib/npg_pipeline/archive/file/generation/seq_alignment.pm
 lib/npg_pipeline/archive/file/qc.pm
 lib/npg_pipeline/archive/file/generation/seqchksum_comparator.pm
@@ -52,7 +45,6 @@ lib/npg_pipeline/pluggable/harold/post_qc_review.pm
 lib/npg_pipeline/roles/accessor.pm
 lib/npg_pipeline/roles/business/base.pm
 lib/npg_pipeline/roles/business/flag_options.pm
-lib/npg_pipeline/roles/business/harold_calibration_reqs.pm
 lib/npg_pipeline/run/folder/link.pm
 lib/npg_tracking/daemon/analysis.pm
 lib/npg_tracking/daemon/archival.pm
@@ -75,18 +67,16 @@ t/15-pipeline_launcher_scripts.t
 t/20-archive-fastqcheck.t
 t/20-archive_auto_qc_to_db.t
 t/20-archive_file-to_irods.t
-t/20-archive_file_generation-illumina2bam.t
 t/20-archive_file_generation-seq_alignment.t
 t/20-archive_folder_generation.t
 t/20-archive_illumina_analysis.t
 t/20-archive_qc.t
 t/20-archive_logs.t
 t/21-references_adapters.t
-t/25-analysis-bustard4pbcb.t
 t/25-analysis-create_lane_tag_file.t
 t/25-analysis-FixConfigFiles.t
 t/25-analysis-split_bam_by_tag.t
-t/25-harold_calibration_bam.t
+t/25-analysis-illumina_basecall_stats.t
 t/30-launcher-status.t
 t/30-run_folder-link.t
 t/35-archive_file_generation-BamClusterCounts.t
@@ -113,7 +103,6 @@ t/bin/software/solexa/jars/Illumina2bam.jar
 t/bin/software/solexa/jars/SplitBamByReadGroup.jar
 t/bin/software/solexa/bin/qc
 t/data/samplesheet_1234.csv
-t/data/illumina2bam/1234_samplesheet.csv
 t/data/qc/1234_samplesheet_amended.csv
 t/data/qc/samplesheet_14353.csv
 t/data/qc/samplesheet_14043.csv

bin/npg_pipeline_central

@@ -23,6 +23,7 @@ Log::Log4perl->easy_init({layout => $layout,
                           file   => $logfile,
                           utf8   => 1});
 
+$p->redirect_stderr();
 $p->main();
 
 0;

bin/npg_pipeline_post_qc_review

@@ -23,6 +23,7 @@ Log::Log4perl->easy_init({layout => $layout,
                           file   => $logfile,
                           utf8   => 1});
 
+$p->redirect_stderr();
 $p->main();
 
 0;

data/config_files/function_list_central.yml

@@ -25,7 +25,6 @@
 - qc_genotype
 - qc_verify_bam_id
 - qc_upstream_tags
-- qc_rna_seqc
 - run_analysis_complete
 - update_ml_warehouse
 - archive_to_irods_samplesheet

data/config_files/function_list_central_qc_run.yml

@@ -22,7 +22,6 @@
 - qc_genotype
 - qc_verify_bam_id
 - qc_upstream_tags
-- qc_rna_seqc
 - run_analysis_complete
 - run_archival_in_progress
 - copy_interop_files_to_irods

data/config_files/parallelisation.yml

@@ -1,5 +1,4 @@
 a:
-    illumina2bam: 1
     illumina_basecall_stats: 1
     p4_stage1_analysis: 1
 b:
@@ -19,7 +18,6 @@ c:
     qc_genotype: 1
     qc_upstream_tags: 1
     qc_verify_bam_id: 1
-    qc_rna_seqc: 1
 d:
     upload_auto_qc_to_qc_database: 1
     upload_fastqcheck_to_qc_database: 1