Snakemake: Cannot find first rule?

Question

Back again with another snakemake query. This time I decided to port my read cleaning and alignment pipeline to snakemake. Repeating the steps from previous question and trying not to make any typo here, I'm now receiving this "error" while trying a dry run using snakemake snakemake -nr -s alignMake:

Building DAG of jobs...
MissingRuleException:
No rule to produce snakemake (if you use input functions make sure that they don't raise unexpected exceptions).

Below is my snakefile:

import os
shell.executable("/bin/bash")

workdir: '/proj/uppstore2018136/publication/jupyterNotebooks'

pathToPEReads = 'raw_data/reads/BL6/totalRNA'
pathToSMReads = 'raw_data/reads/BL6/smallRNA'

pathToHISAT2index = 'indexes/hisat2/reference'
pathToBOWTIE2index = 'indexes/bowtie2/reference'

pathToTemp = 'temp/'
pathToBAM = 'processed_data/BAM'

readsPE, = glob_wildcards('raw_data/reads/BL6/totalRNA/{sample}_1.fastq.gz')
readsSE, = glob_wildcards('raw_data/reads/BL6/smallRNA/{sample}.fq.gz')

samToolsThreads = 6

rule all:
    input:
        expand('processed_data/BAM/{sample}.bam', sample=readsPE),
        expand('processed_data/BAM/{sample}.bam', sample=readsSE)

rule trimgalorePE:
    input:
        fastq1 = pathToPEReads + '{sample}_1.fastq.gz',
        fastq2 = pathToPEReads + '{sample}_2.fastq.gz'
    output:
        output1 = pathToTemp + '{sample}_1_val_1.fq.gz',
        output2 = pathToTemp + '{sample}_2_val_2.fq.gz'
    shell:
        '''
        module load bioinfo-tools
        module load cutadapt
        module load TrimGalore
        trim_galore --quality 20 --paired --length 80 --illumina --stringency 2 --clip_R1 11 --clip_R2 11 -o {pathToTemp} --paired {input.fastq1} {input.fastq2}
        '''

rule trimgaloreSEandDust:
    input:
        fastq = pathToSMReads + '{sample}.fq.gz',
    output:
        output = pathToTemp + '{sample}_trimmed.fq.gz',
    shell:
        '''
        module load bioinfo-tools
        module load cutadapt
        module load TrimGalore
        trim_galore --quality 20 --length 16 --max_length 32 --small_rna --fastqc --stringency 2 -o {pathToTemp} {input.fastq}
        '''

rule align_hisat2:
    input:
        fastq1 = pathToTemp + '{sample}_1_val_1.fq.gz',
        fastq2 = pathToTemp + '{sample}_2_val_2.fq.gz'
    output: 
        output = 'processed_data/BAM/{sample}.bam'
    threads: 10
    shell:
        '''
        module load bioinfo-tools
        module load HISAT2
        module load samtools
        hisat2 -q -p {threads} --no-discordant --no-mixed --rna-strandness RF --dta -x {pathToHISAT2index} -1 {input.fastq1} -2 {input.fastq2} | samtools sort -@ {samToolsThreads} -o {output}
        '''

rule align_bowtie2:
    input:
        fastq = pathToTemp + '{sample}_trimmed.fq.gz'
    output: 
        output = 'processed_data/BAM/{sample}.bam'
    threads: 10
    shell:
        '''
        module load bioinfo-tools
        module load bowtie2
        module load samtools
        bowtie2 --no-unal --end-to-end -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -p {threads} -x {pathToBOWTIE2index} -U {fastq} | samtools sort -@ {samToolsThreads} -o {output}
        '''

rule clean:
    shell:
        '''
        rm temp/*
        '''

I believe it is due snakemake being unable to find the first rule ? Maybe there is something wrong with parsing ? I tested the glob_wildcards and expand function independently and they appear to work properly.

Edit: Here is the directory tree:

.
├── citations
├── doc
├── genome
│   ├── genome.fa
│   └── Mus_musculus.GRCm38.94.gtf
├── indexes
│   ├── bowtie2
│   │   ├── reference.1.bt2
│   │   ├── reference.2.bt2
│   │   ├── reference.3.bt2
│   │   ├── reference.4.bt2
│   │   ├── reference.rev.1.bt2
│   │   └── reference.rev.2.bt2
│   └── hisat2
│       ├── reference.1.ht2
│       ├── reference.2.ht2
│       ├── reference.3.ht2
│       ├── reference.4.ht2
│       ├── reference.5.ht2
│       ├── reference.6.ht2
│       ├── reference.7.ht2
│       └── reference.8.ht2
├── LICENSE
├── notebooks
├── plots
├── processed_data
│   └── BAM
├── raw_data
│   └── reads
│       └── BL6
│           ├── smallRNA
│           │   ├── smBL6_1.fq.gz
│           │   ├── smBL6_2.fq.gz
│           │   └── smBL6_3.fq.gz
│           └── totalRNA
│               ├── EKIxxxx012_1.fastq.gz
│               ├── EKIxxxx012_2.fastq.gz
│               ├── EKIxxxx013_1.fastq.gz
│               ├── EKIxxxx013_2.fastq.gz
│               ├── EKIxxxx014_1.fastq.gz
│               ├── EKIxxxx014_2.fastq.gz
│               ├── ESSxxxx077_1.fastq.gz
│               └── ESSxxxx077_2.fastq.gz
├── README.md
├── recipes
│   ├── alignMake
│   ├── cluster.json
│   ├── indexMake
│   ├── indexMakeScript.out
│   └── indexMakeScript.sh
├── results
├── scripts
├── slurmLogs
│   ├── slurm-6575541.out
│   ├── slurm-6575543.out
│   ├── slurm-6575815.out
│   └── slurm-6580867.out
├── source
└── temp

Answer 1

you are starting snakemake the wrong way.

snakemake snakemake

means "Running the pipeline in Snakefile until you reach a rule named snakemake or a file name snakemake is created."

If your snakefile is called snakemake and this is the pipeline you want to start, the correct syntax would be:

snakemake -s snakemake