Updated to 1.8.2:
(1). Tested local, ftp, and gcp for fastq_server.
(2). Added mhap
(3). Fix bug for qsub

update to 1.8.1:
support mhap

(1). Modularize smk files, and move all smk files into the folder "files/smk".
(2). Move demultiplex.smk into folder "files/smk".
(3). Tested m3c, m3c-multi, mc,mc-multi both on local and GCP
(4). Tested mct.smk
(5). Updated env.yaml and added env_greedy.yaml to fix bug for subread (2.0.1)
(6). Updated cell_parser_hisat_se_summary and columns in mapping summary files

1.7.9
(1). Remove --repeat, using --no-repeat-index in default, because we got different outputs even using the same input and parameter when using --repeat. For example: hisat-3n ~/Ref/hg38/hg38_ucsc_with_chrL -q -1 UWA7648_CX182024_Idg_1_P1-2-K15-A15-R1.trimmed.fq.gz -2 UWA7648_CX182024_Idg_1_P1-2-K15-A15-R2.trimmed.fq.gz --directional-mapping-reverse --base-change C,T --no-spliced-alignment --no-temp-splicesite -t --new-summary --summary-file hisat3n_dna_summary.txt --threads 20| samtools view -b -q 0 -o hisat3n_dna.unsort.bam

1.7.8:
(1). update mapping summary
(2). fix the bug for the input dir in the function summary
(3). update get_fastq_dirs to get_fastq_uids and ran faster
(4). fix bug for directional-mapping-reverse and directional-mapping in hisat_3n_single_end_mapping_dna_mode
(5). use cell_parser_hisat_summary snm3c_summary for /bam/.hisat3n_dna_split_reads_summary.R1.txt and /bam/.hisat3n_dna_split_reads_summary.R2.txt

1.7.7: run salk010 mapping succeed, merge lanes before demultiplex, added cell_qc in the demultiplex rule

1.7.6: merge lanes after demultiplex, use cat to merge lane, instead of gzip -cd

update to 1.7.5:ran salk10_test succeed, support demultiplex on GCP

update to 1.7.4: run test demultiplex and mapping for BICAN Novaseq test fastq succeed

(1). Fix some bugs, such as fastq name parse, 4 lanes to 8 lanes
(2). Support both local and GCP for demultiplex and mapping